Re: [Freesurfer] R: Re: Import FS data to FSL
Try mri_annotation2label. On Wed, 25 Sep 2013, std...@virgilio.it wrote: For FSL guide: I should transforms a group of labels into a surface Usage: label2surf -s surface -o outputsurface -l labels Compulsory arguments (You MUST set one or more of): -s,--surf input surface -o,--out output surface -l,--labels ascii list of label files Optional arguments (You may optionally specify one or more of): -v,--verbose switch on diagnostic messages -h,--help display this message but I should create a lh/rh.frontal.label and use it for label2surf. With mdi_binarize I can create .nii.gz but no .label. Is that correct? How I can do it? Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 25-set-2013 17.49 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Import FS data to FSL 1 - Yes. 2 - You can use mri_aparc2aseg to grow the cortical labels into the white matter (say, by 2mm). The file that it will produce will be a volume file, so then you just run mri_binarize to extract specific labels. Make sure you save them in nifti format for FSL. On Wed, 25 Sep 2013, std...@virgilio.it wrote: Hi list, I have 2 questions, please. 1-The bedpostX that I have run for TRACULA could be used for PROBTRACKX (FSL)? 2-I'd like to export cortical masks from FS to FSL. An option is mri_binarize but this way failed in probtrackx (fsl). FSL list have advised me that I should use label2surf command to convert label to surface files. Where could find the .label (according to FreeSurferColorLUT.txt) to build mask of frontal, parietal, motor, sensor, temporal and occipital lobes? Do you have other ways that you advise me? Thanks, Stefano The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula bval and bvec
Hi Gari - Sorry, right now the assumption is that the gradient vectors are the same for all subjects. How different are they? a.y On Wed, 25 Sep 2013, Garikoitz Lerma-Usabiaga wrote: Hi Anastasia,I am setting up the dmrirc file to run Tracula. I am using Siemens Dicoms, so I did not specify any setting for bval and bvec, but when trac-all -prep starts running it gives the following error: mv: cannot stat 'paths.../SubjectID/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory Ok, so I understand that our problem is that we don't have MGH Siemens Dicom. So I used dcm2nii to convert it to .nii files and each conversion gives me a SubjectID.bval and SubjectID.bvec. Every .bval is the same file, but every .bvec file is a different one. I can edit set dcm_list = to include all the newly created .nii files, but My question is: - How can I specify every .bvec value for every subject? In the dmrirc file everything I see is a set bvecfile = option. Thank you very much, Gari ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] question about TRACULA
Hi Lucia - The error occurs when the text file with the gradient vectors is being processed. Can you please attach that file? Thanks, a.y On Fri, 20 Sep 2013, Lucia Billeci wrote: Dear Madam/Sir, I am trying to applying TRACULA on my data but when I run the following command: trac-all -prep -c /Users/Desktop/FreesurferData/SUBJECT1/dmrirc_subject1 after some processing I obtain the following error xfmrot /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/dwi.ecclog /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs.norot /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs printf: .97: expected numeric value printf: .002040: expected numeric value printf: .001230: expected numeric value printf: 8.010424: not completely converted printf: -4.983286: not completely converted printf: -.000389: expected numeric value printf: -.759652: expected numeric value printf: -5.031242: not completely converted printf: 8.006841: not completely converted printf: 7.864457: not completely converted printf: 3.131627: not completely converted printf: -3.216084: not completely converted printf: -1.957800: not completely converted printf: 7.048668: not completely converted printf: 5.956787: not completely converted printf: -7.998542: not completely converted printf: 1.996216: not completely converted printf: 4.004804: not completely converted printf: 7.008384: not completely converted printf: -2.985687: not completely converted printf: 3.996015: not completely converted printf: -.986002: expected numeric value printf: -9.000231: not completely converted printf: .153834: expected numeric value printf: 7.937660: not completely converted printf: .875656: expected numeric value printf: 4.150514: not completely converted printf: -2.115330: not completely converted printf: 8.962086: not completely converted printf: 2.050965: not completely converted printf: 5.758588: not completely converted printf: 8.092588: not completely converted printf: -4.165180: not completely converted printf: 4.753098: not completely converted printf: 5.079427: not completely converted printf: -6.132490: not completely converted printf: -4.21: not completely converted printf: 4.007709: not completely converted printf: 6.995579: not completely converted printf: -4.879465: not completely converted printf: -7.066532: not completely converted printf: 1.120257: not completely converted printf: -5.186508: not completely converted printf: -2.066011: not completely converted printf: -7.863320: not completely converted printf: -5.008038: not completely converted printf: 5.995846: not completely converted printf: 3.996178: not completely converted printf: 5.717007: not completely converted printf: 5.121524: not completely converted printf: -7.147437: not completely converted printf: 1.743757: not completely converted printf: 7.060581: not completely converted printf: -9.005971: not completely converted printf: -4.251174: not completely converted printf: 5.953915: not completely converted printf: -4.845450: not completely converted printf: -4.010977: not completely converted printf: -8.049025: not completely converted printf: -2.850488: not completely converted printf: 4.005690: not completely converted printf: -7.995851: not completely converted printf: 1.010371: not completely converted printf: -5.118400: not completely converted printf: -4.070279: not completely converted printf: -6.872761: not completely converted printf: 8.143535: not completely converted printf: 4.835332: not completely converted printf: 1.817269: not completely converted printf: 2.268035: not completely converted printf: -2.989943: not completely converted printf: 7.931980: not completely converted printf: -4.199139: not completely converted printf: -3.025800: not completely converted printf: -8.900100: not completely converted grep: /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/dcminfo.dat: No such file or directory fslroi /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/dwi.nii.gz /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/lowb.nii.gz 0 Usage: fslroi input output xmin xsize ymin ysize zmin zsize fslroi input output tmin tsize fslroi input output xmin xsize ymin ysize zmin zsize tmin tsize Note: indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for that dimension. Could you please give me some help? Thanks a lot Best Regards Lucia Billeci_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa ITALY Tel: +39-0506213204 e-mail: lucia.bill...@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the
Re: [Freesurfer] Tracula and Qdec
Hi Alan - Glad to hear that you have an interesting finding! Can you describe what type of thing you want to visualize a bit more? If it's not on the surface, freeview will more likely do the trick rather than qdec. a.y On Fri, 13 Sep 2013, Alan Francis wrote: Hi Anastasia and FreeSurfers: Is it possible to model Tracula data on Qdec? I have some interesting findings in FA and AD between two groups that I am hoping to visually represent on a single brain. Any advice would be deeply appreciated. thank you, Alan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula and Qdec
Hi Alan - Are you looking at average AD over the whole tract, or AD along the tract? a.y On Fri, 13 Sep 2013, Alan Francis wrote: Hi Anastasia: Thanks for your quick reply. We would like to look at the left and right Cortico-spinal tract AD between the groups. Also left and right ATR AD if possible. thanks again, Alan On Fri, Sep 13, 2013 at 10:53 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Alan - Glad to hear that you have an interesting finding! Can you describe what type of thing you want to visualize a bit more? If it's not on the surface, freeview will more likely do the trick rather than qdec. a.y On Fri, 13 Sep 2013, Alan Francis wrote: Hi Anastasia and FreeSurfers: Is it possible to model Tracula data on Qdec? I have some interesting findings in FA and AD between two groups that I am hoping to visually represent on a single brain. Any advice would be deeply appreciated. thank you, Alan The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Tracula and Qdec
I see, then it's an ROI analysis, where the tract is the ROI. Isn't it sufficient for you to visualize the tracts in an example subject with the -tv option in freeview? What would you like to do beyond that? On Fri, 13 Sep 2013, Alan Francis wrote: Hi Anastasia: I am looking at Average AD in these tracts. thanks, Alan On Fri, Sep 13, 2013 at 11:37 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Alan - Are you looking at average AD over the whole tract, or AD along the tract? a.y On Fri, 13 Sep 2013, Alan Francis wrote: Hi Anastasia: Thanks for your quick reply. We would like to look at the left and right Cortico-spinal tract AD between the groups. Also left and right ATR AD if possible. thanks again, Alan On Fri, Sep 13, 2013 at 10:53 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Alan - Glad to hear that you have an interesting finding! Can you describe what type of thing you want to visualize a bit more? If it's not on the surface, freeview will more likely do the trick rather than qdec. a.y On Fri, 13 Sep 2013, Alan Francis wrote: Hi Anastasia and FreeSurfers: Is it possible to model Tracula data on Qdec? I have some interesting findings in FA and AD between two groups that I am hoping to visually represent on a single brain. Any advice would be deeply appreciated. thank you, Alan The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula and Qdec
Hi Alan - Sorry, tracula doesn't do voxel-based analyses, only tract-based. a.y On Fri, 13 Sep 2013, Alan Francis wrote: Hi Anastasia: Yes I generated the left CST on a single subject using the Freeview -tv option. But my boss wanted to know if it was possible to do a voxelwise group analysis and show mean differences on a single inflated brain. thanks, Alan On Fri, Sep 13, 2013 at 11:43 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: I see, then it's an ROI analysis, where the tract is the ROI. Isn't it sufficient for you to visualize the tracts in an example subject with the -tv option in freeview? What would you like to do beyond that? On Fri, 13 Sep 2013, Alan Francis wrote: Hi Anastasia: I am looking at Average AD in these tracts. thanks, Alan On Fri, Sep 13, 2013 at 11:37 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Alan - Are you looking at average AD over the whole tract, or AD along the tract? a.y On Fri, 13 Sep 2013, Alan Francis wrote: Hi Anastasia: Thanks for your quick reply. We would like to look at the left and right Cortico-spinal tract AD between the groups. Also left and right ATR AD if possible. thanks again, Alan On Fri, Sep 13, 2013 at 10:53 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Alan - Glad to hear that you have an interesting finding! Can you describe what type of thing you want to visualize a bit more? If it's not on the surface, freeview will more likely do the trick rather than qdec. a.y On Fri, 13 Sep 2013, Alan Francis wrote: Hi Anastasia and FreeSurfers: Is it possible to model Tracula data on Qdec? I have some interesting findings in FA and AD between two groups that I am hoping to visually represent on a single brain. Any advice would be deeply appreciated. thank you, Alan The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Cortical labels for WM seeding
Hi Sean - Do you mean that the streamlines go through non-brain voxels? You could you a slightly dilated version of the aparc+aseg as a mask. You can use bbregister to map it to the subject's DWI space. a.y On Mon, 9 Sep 2013, Sean Hatton wrote: Hello FS Gurus, I would like to export FS labels as seed regions for deterministic tractography in TrackVis (probabilistic is not appropriate in this investigation). I run mri_label2vol with “--proj abs -4 0 .1” to try and grow the label into the WM and exclude GM. While I get a biologically plausible ROIs and plenty of good streamlines, I do get some stray streamlines that jump across the sulci into adjacent gyri which (I have read) is an artefact of seeding from GM. Have I got the right approach? Should I create an inverse intracranial volume mask as an exclusion mask? Something else? Kind regards, Sean Hatton Brain Mind Research Institute University of Sydney, Australia. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Cortical labels for WM seeding
I'd probably try GM plus a (DWI-sized) voxel or so into the WM. On Mon, 9 Sep 2013, Sean Hatton wrote: Great, I will give that a shot. In the seeding ROI should I combine the gm and wm labels or is the GM sufficient to encapsulate, say, the superior temporal gurus GM and WM? Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Sean - Do you mean that the streamlines go through non-brain voxels? You could you a slightly dilated version of the aparc+aseg as a mask. You can use bbregister to map it to the subject's DWI space. a.y On Mon, 9 Sep 2013, Sean Hatton wrote: Hello FS Gurus, I would like to export FS labels as seed regions for deterministic tractography in TrackVis (probabilistic is not appropriate in this investigation). I run mri_label2vol with “--proj abs -4 0 .1” to try and grow the label into the WM and exclude GM. While I get a biologically plausible ROIs and plenty of good streamlines, I do get some stray streamlines that jump across the sulci into adjacent gyri which (I have read) is an artefact of seeding from GM. Have I got the right approach? Should I create an inverse intracranial volume mask as an exclusion mask? Something else? Kind regards, Sean Hatton Brain Mind Research Institute University of Sydney, Australia. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula error - unknown queue long.q, short.q
Hm, this looks uniformly bad. Have you checked that the gradient directions are correct? You can check that by looking at the eigenvectors from the tensor fit that's done as part of the preprocessing. Although tracula doesn't use tensors for tractography, it's a quick way to check that your inputs are correct. In fslview, overlay dmri/dtifit_V1.nii.gz on dmri/dtifit_FA.nii.gz, and display dtifit_V1 as lines. Then make sure that the lines follow the basic anatomy e.g. in the corpus callosum (L-R), cingulum (A-P), corticospinal tract (I-S). On Thu, 5 Sep 2013, Joana Braga Pereira wrote: Hi, Thanks for all the replies, I solved the problem I had before. However, after finishing the Tracula pre-processing steps I tried to visualize the tracts by typing: freeview -tv CTR01/dpath/merged_avg33_mni_bbr.mgz And, as you can see in the picture I'm attaching to this email, it seems the tracts were not properly reconstructed. Does anyone know why? Should I make some changes and for example set the control points differently from the ones proposed on Tracula website? Any help will be greatly appreciated! Thanks, joana 2013/9/2 Watson, Christopher christopher.wat...@childrens.harvard.edu Indeed. It's actually really easy to set up, too. From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Monday, September 02, 2013 3:46 PM To: Watson, Christopher Cc: Joana Braga Pereira; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula error - unknown queue long.q, short.q Thanks for the pointers, Chris. I'd call it an opportunity for FSL customization rather than an FSL problem per se :o) On Mon, 2 Sep 2013, Watson, Christopher wrote: This is an FSL problem. You can try the FSL list, and check out some links: https://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html http://chrisfilo.tumblr.com/post/579493955/how-to-configure-sun-grid-engine-for-fsl-under-ubuntu From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Joana Braga Pereira [jbragapere...@gmail.com] Sent: Monday, September 02, 2013 9:53 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Tracula error - unknown queue long.q, short.q Dear Anastasia and FreeSurfers, I was preprocessing some data using tracula and found this error after running trac-all -bedp -c dmrirc: INFO: SUBJECTS_DIR is /data-02/joana/Last INFO: Diffusion root is /data-02/joana/tracula/ Actual FREESURFER_HOME /usr/local/freesurfer-5.3 WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /data-02/joana/tracula//XXX/dmri subjectdir is /data-02/joana/tracula/XXX/dmri Making bedpostx directory structure Queuing preprocessing stages Unable to run job: Job was rejected because job requests unknown queue short.q. Exiting. Queuing parallel processing stage Unable to run job: Job was rejected because job requests unknown queue long.q. Exiting. Queuing post processing stage Unable to run job: denied: 60 is not a valid object name (cannot start with a digit) Job was rejected because job requests unknown queue long.q. Exiting. Type /data-02/joana/tracula/3119/dmri.bedpostX/monitor to show progress. Type /data-02/joana/tracula/3119/dmri.bedpostX/cancel to terminate all the queued tasks. You will get an email at the end of the post-processing stage. So far no slices have been processed. Does anyone know how to solve it? Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error
Re: [Freesurfer] Tracula error - unknown queue long.q, short.q
Yes, it does look from the images like the L-R and A-P directions are swapped. So you can switch around the x and y columns of you gradient table and rerun the preprocessing and check the eigenvectors again. It may be some other combination of swaps that needs to be done, but the x and y looks like the most likely to me. For sure the gradient table is wrong. On Thu, 5 Sep 2013, Joana Braga Pereira wrote: Thanks! I've uploaded those files as well as dmrirc and bvecs and bvals. Let me know what you think. 2013/9/5 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Indeed, they look like they're oriented A-P in the corpus callosum and L-R in the cinglulum, when it should be the opposite obviously. This'd mean you'd have to swap things in the gradient table. It's hard to tell for sure from the screenshot though. If you upload the dtifit_FA and dtifit_V1 volumes for me here, I'll look at them: https://gate.nmr.mgh.harvard.edu/filedrop2/ On Thu, 5 Sep 2013, Joana Braga Pereira wrote: Hi Anastasia, Thanks! I checked dtifit_FA and did the overlay with V1. They don't look ok to me (see attached picture). Any suggestions on how to solve this? Perhaps by modifying any of the previous steps? Thanks! 2013/9/5 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Hm, this looks uniformly bad. Have you checked that the gradient directions are correct? You can check that by looking at the eigenvectors from the tensor fit that's done as part of the preprocessing. Although tracula doesn't use tensors for tractography, it's a quick way to check that your inputs are correct. In fslview, overlay dmri/dtifit_V1.nii.gz on dmri/dtifit_FA.nii.gz, and display dtifit_V1 as lines. Then make sure that the lines follow the basic anatomy e.g. in the corpus callosum (L-R), cingulum (A-P), corticospinal tract (I-S). On Thu, 5 Sep 2013, Joana Braga Pereira wrote: Hi, Thanks for all the replies, I solved the problem I had before. However, after finishing the Tracula pre-processing steps I tried to visualize the tracts by typing: freeview -tv CTR01/dpath/merged_avg33_mni_bbr.mgz And, as you can see in the picture I'm attaching to this email, it seems the tracts were not properly reconstructed. Does anyone know why? Should I make some changes and for example set the control points differently from the ones proposed on Tracula website? Any help will be greatly appreciated! Thanks, joana 2013/9/2 Watson, Christopher christopher.wat...@childrens.harvard.edu Indeed. It's actually really easy to set up, too. From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Monday, September 02, 2013 3:46 PM To: Watson, Christopher Cc: Joana Braga Pereira; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula error - unknown queue long.q, short.q Thanks for the pointers, Chris. I'd call it an opportunity for FSL customization rather than an FSL problem per se :o) On Mon, 2 Sep 2013, Watson, Christopher wrote: This is an FSL problem. You can try the FSL list, and check out some links: https://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html http://chrisfilo.tumblr.com/post/579493955/how-to-configure-sun-grid-engine-for-fsl-under-ubuntu From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Joana Braga Pereira [jbragapere...@gmail.com
Re: [Freesurfer] Tracula error - unknown queue long.q, short.q
Indeed, they look like they're oriented A-P in the corpus callosum and L-R in the cinglulum, when it should be the opposite obviously. This'd mean you'd have to swap things in the gradient table. It's hard to tell for sure from the screenshot though. If you upload the dtifit_FA and dtifit_V1 volumes for me here, I'll look at them: https://gate.nmr.mgh.harvard.edu/filedrop2/ On Thu, 5 Sep 2013, Joana Braga Pereira wrote: Hi Anastasia, Thanks! I checked dtifit_FA and did the overlay with V1. They don't look ok to me (see attached picture). Any suggestions on how to solve this? Perhaps by modifying any of the previous steps? Thanks! 2013/9/5 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Hm, this looks uniformly bad. Have you checked that the gradient directions are correct? You can check that by looking at the eigenvectors from the tensor fit that's done as part of the preprocessing. Although tracula doesn't use tensors for tractography, it's a quick way to check that your inputs are correct. In fslview, overlay dmri/dtifit_V1.nii.gz on dmri/dtifit_FA.nii.gz, and display dtifit_V1 as lines. Then make sure that the lines follow the basic anatomy e.g. in the corpus callosum (L-R), cingulum (A-P), corticospinal tract (I-S). On Thu, 5 Sep 2013, Joana Braga Pereira wrote: Hi, Thanks for all the replies, I solved the problem I had before. However, after finishing the Tracula pre-processing steps I tried to visualize the tracts by typing: freeview -tv CTR01/dpath/merged_avg33_mni_bbr.mgz And, as you can see in the picture I'm attaching to this email, it seems the tracts were not properly reconstructed. Does anyone know why? Should I make some changes and for example set the control points differently from the ones proposed on Tracula website? Any help will be greatly appreciated! Thanks, joana 2013/9/2 Watson, Christopher christopher.wat...@childrens.harvard.edu Indeed. It's actually really easy to set up, too. From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Monday, September 02, 2013 3:46 PM To: Watson, Christopher Cc: Joana Braga Pereira; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula error - unknown queue long.q, short.q Thanks for the pointers, Chris. I'd call it an opportunity for FSL customization rather than an FSL problem per se :o) On Mon, 2 Sep 2013, Watson, Christopher wrote: This is an FSL problem. You can try the FSL list, and check out some links: https://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html http://chrisfilo.tumblr.com/post/579493955/how-to-configure-sun-grid-engine-for-fsl-under-ubuntu From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Joana Braga Pereira [jbragapere...@gmail.com] Sent: Monday, September 02, 2013 9:53 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Tracula error - unknown queue long.q, short.q Dear Anastasia and FreeSurfers, I was preprocessing some data using tracula and found this error after running trac-all -bedp -c dmrirc: INFO: SUBJECTS_DIR is /data-02/joana/Last INFO: Diffusion root is /data-02/joana/tracula/ Actual FREESURFER_HOME /usr/local/freesurfer-5.3 WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /data-02/joana/tracula//XXX/dmri subjectdir is /data-02/joana/tracula/XXX/dmri Making bedpostx directory structure Queuing preprocessing stages Unable to run job: Job was rejected because job requests unknown queue short.q. Exiting. Queuing parallel processing stage Unable to run job: Job was rejected because job requests unknown queue long.q. Exiting. Queuing post processing stage
Re: [Freesurfer] Tracula threshold path
Hi Celine - The path.pd.nii.gz file contains the full probability distribution without any thresholding. This distribution, as with any probabilistic tractography method, expresses the amount of uncertainty in which is the path of most coherent diffusion between the two end regions. (In tracula's case, it's actually both most coherent diffusion and most consistent with the anatomy of the CST, or whichever pathway, based on the atlas.) If in a patient there's widespread degeneration over the entire path, this could manifest itself as more uncertainty and hence a more spread out distribution. So depending on the variability among your subjects you could get wider or narrower pathway ROIs. If you find that a threshold based on path.pd.nii.gz alone is not consistent for your purposes, you could try combining it with an FA threshold. Hope this helps, a.y On Wed, 4 Sep 2013, cel...@nmr.mgh.harvard.edu wrote: Dear experts, I read some previous answers about the thresholding of the paths obtained after tracula process, but I am not completely sure I had the right answer. I will need to get an roi from a path for example the cortico-spinal tract that will be consistent amongst patients. I will further use this roi to calculate the lesion volume (my subjects are patients with MS) within a specific path. My question is: is the path.pd.nii.gz file already threshold or should I threshold it to a specific value? If I use the same threshold for each subject for example at 10% of the maximum value, will I obtain an ROI that is consistent among subjects or is is possible that I would get a very thin CST in some subjects, or a very wide cst for example? Thanks for your help Celine ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula error - unknown queue long.q, short.q
Hi Joana - What system are you running this on? a.y On Mon, 2 Sep 2013, Joana Braga Pereira wrote: Dear Anastasia and FreeSurfers, I was preprocessing some data using tracula and found this error after running trac-all -bedp -c dmrirc: INFO: SUBJECTS_DIR is /data-02/joana/Last INFO: Diffusion root is /data-02/joana/tracula/ Actual FREESURFER_HOME /usr/local/freesurfer-5.3 WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /data-02/joana/tracula//XXX/dmri subjectdir is /data-02/joana/tracula/XXX/dmri Making bedpostx directory structure Queuing preprocessing stages Unable to run job: Job was rejected because job requests unknown queue short.q. Exiting. Queuing parallel processing stage Unable to run job: Job was rejected because job requests unknown queue long.q. Exiting. Queuing post processing stage Unable to run job: denied: 60 is not a valid object name (cannot start with a digit) Job was rejected because job requests unknown queue long.q. Exiting. Type /data-02/joana/tracula/3119/dmri.bedpostX/monitor to show progress. Type /data-02/joana/tracula/3119/dmri.bedpostX/cancel to terminate all the queued tasks. You will get an email at the end of the post-processing stage. So far no slices have been processed. Does anyone know how to solve it? Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula error - unknown queue long.q, short.q
Thanks for the pointers, Chris. I'd call it an opportunity for FSL customization rather than an FSL problem per se :o) On Mon, 2 Sep 2013, Watson, Christopher wrote: This is an FSL problem. You can try the FSL list, and check out some links: https://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html http://chrisfilo.tumblr.com/post/579493955/how-to-configure-sun-grid-engine-for-fsl-under-ubuntu From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Joana Braga Pereira [jbragapere...@gmail.com] Sent: Monday, September 02, 2013 9:53 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Tracula error - unknown queue long.q, short.q Dear Anastasia and FreeSurfers, I was preprocessing some data using tracula and found this error after running trac-all -bedp -c dmrirc: INFO: SUBJECTS_DIR is /data-02/joana/Last INFO: Diffusion root is /data-02/joana/tracula/ Actual FREESURFER_HOME /usr/local/freesurfer-5.3 WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /data-02/joana/tracula//XXX/dmri subjectdir is /data-02/joana/tracula/XXX/dmri Making bedpostx directory structure Queuing preprocessing stages Unable to run job: Job was rejected because job requests unknown queue short.q. Exiting. Queuing parallel processing stage Unable to run job: Job was rejected because job requests unknown queue long.q. Exiting. Queuing post processing stage Unable to run job: denied: 60 is not a valid object name (cannot start with a digit) Job was rejected because job requests unknown queue long.q. Exiting. Type /data-02/joana/tracula/3119/dmri.bedpostX/monitor to show progress. Type /data-02/joana/tracula/3119/dmri.bedpostX/cancel to terminate all the queued tasks. You will get an email at the end of the post-processing stage. So far no slices have been processed. Does anyone know how to solve it? Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Clarification regarding bvec processing in TRACULA
Nope, there's no flipping in tracula. But, *both* the gradient vectors and the DWIs are converted to LAS orientation as the first step in the preprocessing. This makes the FSL tools that are run later in the preprocessing (dtifit and bedpostx) run smoothly without any flipping. On Mon, 26 Aug 2013, Salil Soman wrote: Hi, After much searching, it appears to be pretty uniform that the product DTI sequence performed on GE requires the y gradient to be flipped. For the datasets with which I am working diffusion toolkit, vistalab and exploredti all require the y gradient to be flipped. However, Tracula makes appropriate outputs when I give it the default gradient table without flipping Y. When I flip Y and run it through Tracula, the forceps major is inverted (noted by checking the overlay of dtifit_fa and dtifit_V1 using fslview and by using TVglyphView using DTI-TK. I suspect that somehow Tracula is flipping the Y sign for the gradient (while the other programs I mentioned do not) - can anyone confirm this? Thanks! -Sal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] [tracula] error running trac-all -prep
Hi Florian - My guess is that everything ran fine and you don't need to change anything else. Check that all the output files were created in the dmri.bedpostX directory: http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_bedpostx.html a.y On Thu, 22 Aug 2013, Borsodi Florian wrote: Hi Anastasia, This Ubuntu-related error is a tricky one. I changed the first line in those files you told me and reran trac-all. All three steps of trac-all ran without any errrors. I checked the FA maps and the MNI registration and everything looks fine. After running trac-all -bedp, the step stopped with the following line: Queuing post processing stage /usr/local/freesurfer/bin/bedpostx_mgh: line 439: 9381 Terminated ${subjdir}.bedpostX/monitor. I think it's fine, because line 439 is the last line of the script, so it worked well. Maybe I have to change all .sh in the files to .bash to get all messages. Thank you so much for your big help. I hope I didn't cause you much trouble with my problems and questions. Sincerely, Florian Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 20.08.13 17.56 Uhr This is an Ubuntu-related error that has surfaced recently because in Ubuntu /bin/sh is not a bash shell any more. To get around this, you can edit the first line of the scripts $FREESURFER_HOME/bin/bedpostx_mgh and $FREESURFER_HOME/bin/fsl_sub_mgh. You'll have to replace /bin/sh with /bin/bash on the first line of those two scripts. On Tue, 20 Aug 2013, Borsodi Florian wrote: Hi Anastasia, Yes, i am running this on ubuntu 12.04. Sincerely, Florian Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 20.08.13 17.38 Uhr Hi Florian - Are you running this on an ubuntu system by any chance? a.y On Tue, 20 Aug 2013, Borsodi Florian wrote: Hi Anastasia, Thank you for your help. I changed the commas in /dmri/bvecs to dots and reran trac-all. But the command xfmrot changed the dots back to commas. So, I changed our system language from de_AUT.UTF-8 to en_US.UTF-8 and reran trac-all. After changing the system language everything was genereted correctly and trac-all -prep ran without any errors. I'm so glad. Then, I started the next step trac-all -bedp and got a syntax error /usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: ( unexpected. I also attached the the logfile. I was reading about this error in the mail archive. Would I have to run bedpostx outside of tracula ? Sincerely, Florian Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 19.08.13 17.54 Uhr Hi Florian - Can you please change the decimal commas to points and try again? a.y On Mon, 19 Aug 2013, Borsodi Florian wrote: Hi Anastasia, Here are the bvec and bval files you asked me about. Sincerely, Florian Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 18.08.13 22.52 Uhr Hi Florian - Can you please also attach the bvecs/bvals files from the dmri directory? Thanks, a.y On Sun, 18 Aug 2013, Borsodi Florian wrote: Hi Anastasia, Thanks for your help. I renamed the directories and reran trac-all. It worked for the moment. However, then I got another error: bvecs and bvals don't have the same number of entries. I don't know why, because they actually have the same number of entries. I attached the logfile so that you may see what is going on. The error occours at line 1463. Thank you in advance for your help. Sincerely, Florian Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 15.08.13 18.01 Uhr Hi Florian - I see what's going on. Can you please rename the directory /data/physics/florian/nii into something that doesn't include nii, and rerun? Because nii is a file extension, this confuses some of the scripts. Thanks, a.y On Thu, 15 Aug 2013, Borsodi Florian wrote: Hi Anastasia I ran the command you sent me and it runs without any errors. I also attached the command line for you. Furthermore i ran data with 12 diffusion directions and i keep getting the same kind of problems. sincerely Florian Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 02.08.13 19.59 Uhr Hi Florian - Can you please run this command directly on the command line and see if there are any errors? flip4fsl /data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.nii.gz /data/physics/florian/nii/102485074_20080319/dmri/dwi_orig_flip.nii.gz Thanks, a.y On Fri, 2 Aug 2013, Borsodi Florian wrote: Hi Anastasia Thank you for your answer. Yes, those files exist. I also extracted the bvec an bval files with anotther software then dcm2nii and i keep getting the same kind of error. Also, about the 6 diffusion direction, those data i sent you
Re: [Freesurfer] gradient table question for Tracula
Hi Sal - Sorry but I don't know what the interaction of dcm2nii and GE dicom headers is. If anyone else on the list uses dcm2nii on GE dicoms, they can chime in. To make sure the gradient table is right, I'd always check the primary eigenvector directions (overlaying dmri/dtifit_V1.nii.gz on dmri/dtifit_FA.nii.gz and viewing the former as lines). You just need to do this on one of the data sets from your sequence just to make sure they're oriented correctly. Also, if the gradient vectors need flipping, the tracts from tracula will come out looking visibly wrong. So you'll know that something went wrong. Hope this helps, a.y On Thu, 22 Aug 2013, Salil Soman wrote: Hi Anastasia, A question I had about the gradient tables for Tracula - I recently came across this passage from Hui Zhang: To correct for any errors that you identify, you need to first modify the gradient table, then repeat the tensor reconstruction. The modification of the gradient table typically involves flipping the signs of the x or y component of all gradient vectors. To determine the correct flipping of the signs in a systematic way, it is necessary to understand why this happens. The reason is that the gradient directions are always defined with respect to some right-handed frame of reference, while the frame of reference of the acquired image data is typically NOT right-handed. This mismatch is the cause of the problem. The sign flipping intends to fix this mismatch and the key is to identify the difference between the two frames of reference in question. In our experience, if the data is acquired on SIEMENS scanners, the signs of x gradient components need to be flipped; for GE scanners, it is usually the y components.(from http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.Visua lizationTool). Does this mean that the gradient tables i get from dcm2nii need to have the Y component flipped for my GE acquisitions or is this adjusted in the tracula processing? Thank you. -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Track stats and covariates
Definitely age. You don't need to adjust for volume since these are not volume/area/length measures that you're comparing. You should also check for any group differences in motion before you proceed and make sure your groups are matched in terms of motion. If you do separate t-tests for each tract, you'll need to adjust for multiple comparisons (by the number of tracts). On Tue, 20 Aug 2013, Alan Francis wrote: Hi Anastasia: Just a quick question. When comparing FA, AD, RD etc between 2 groups, do we need to use covariates like Intra Cranial volume or AGE? If the answer is no, should I do an ANOVA or will T tests be sufficient? thank you, Alan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] [tracula] error running trac-all -prep
Hi Florian - Are you running this on an ubuntu system by any chance? a.y On Tue, 20 Aug 2013, Borsodi Florian wrote: Hi Anastasia, Thank you for your help. I changed the commas in /dmri/bvecs to dots and reran trac-all. But the command xfmrot changed the dots back to commas. So, I changed our system language from de_AUT.UTF-8 to en_US.UTF-8 and reran trac-all. After changing the system language everything was genereted correctly and trac-all -prep ran without any errors. I'm so glad. Then, I started the next step trac-all -bedp and got a syntax error /usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: ( unexpected. I also attached the the logfile. I was reading about this error in the mail archive. Would I have to run bedpostx outside of tracula ? Sincerely, Florian Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 19.08.13 17.54 Uhr Hi Florian - Can you please change the decimal commas to points and try again? a.y On Mon, 19 Aug 2013, Borsodi Florian wrote: Hi Anastasia, Here are the bvec and bval files you asked me about. Sincerely, Florian Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 18.08.13 22.52 Uhr Hi Florian - Can you please also attach the bvecs/bvals files from the dmri directory? Thanks, a.y On Sun, 18 Aug 2013, Borsodi Florian wrote: Hi Anastasia, Thanks for your help. I renamed the directories and reran trac-all. It worked for the moment. However, then I got another error: bvecs and bvals don't have the same number of entries. I don't know why, because they actually have the same number of entries. I attached the logfile so that you may see what is going on. The error occours at line 1463. Thank you in advance for your help. Sincerely, Florian Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 15.08.13 18.01 Uhr Hi Florian - I see what's going on. Can you please rename the directory /data/physics/florian/nii into something that doesn't include nii, and rerun? Because nii is a file extension, this confuses some of the scripts. Thanks, a.y On Thu, 15 Aug 2013, Borsodi Florian wrote: Hi Anastasia I ran the command you sent me and it runs without any errors. I also attached the command line for you. Furthermore i ran data with 12 diffusion directions and i keep getting the same kind of problems. sincerely Florian Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 02.08.13 19.59 Uhr Hi Florian - Can you please run this command directly on the command line and see if there are any errors? flip4fsl /data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.nii.gz /data/physics/florian/nii/102485074_20080319/dmri/dwi_orig_flip.nii.gz Thanks, a.y On Fri, 2 Aug 2013, Borsodi Florian wrote: Hi Anastasia Thank you for your answer. Yes, those files exist. I also extracted the bvec an bval files with anotther software then dcm2nii and i keep getting the same kind of error. Also, about the 6 diffusion direction, those data i sent you, are just testdata for running tracula. sincerely Florian Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 02.08.13 0.41 Uhr Hi Florian - Do these files exist? /data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.mghdti.bvec s /data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.mghdti.bval s The format of the bvecs and bvals that you sent seems fine, but (and this has nothing to do with the error you're getting) I have to warn you that you may not be able to get good results running probabilistic tractography on this data. It looks like you're acquiring the same 6 diffusion directions, repeated 8 times. Six directions is the absolute minimum for reconstructing the tensor model, but will probably not be sufficient for the crossing fiber model that bedpostx reconstructs (and is used by tracula). Your scan time is better spent acquiring 48 different directions, rather than the same 6 directions 8 times. a.y On Mon, 29 Jul 2013, Borsodi Florian wrote: Hello, I have been trying to run tracula on my data and i keep getting the same kind of error repeatedly. For my imput I am using dicoms from a Siemens scanner with a stadard diffusion protocol. However, tracula cannot read the bvec and bval data out of the dicom header. Therefore, I implemented bvec and bval files into the config file. After doing so, I got the error which says that tracula cannot find the dwi_orig_flip.mghdti.bvecs and dwi_orig_flip.mghdti.bvals files. I have tried many options, but still cannot find a solution. I am hoping to get some troubleshooting help. I have atteched my log- and config- files, as well as my bvec and bval files
Re: [Freesurfer] [tracula] error running trac-all -prep
This is an Ubuntu-related error that has surfaced recently because in Ubuntu /bin/sh is not a bash shell any more. To get around this, you can edit the first line of the scripts $FREESURFER_HOME/bin/bedpostx_mgh and $FREESURFER_HOME/bin/fsl_sub_mgh. You'll have to replace /bin/sh with /bin/bash on the first line of those two scripts. On Tue, 20 Aug 2013, Borsodi Florian wrote: Hi Anastasia, Yes, i am running this on ubuntu 12.04. Sincerely, Florian Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 20.08.13 17.38 Uhr Hi Florian - Are you running this on an ubuntu system by any chance? a.y On Tue, 20 Aug 2013, Borsodi Florian wrote: Hi Anastasia, Thank you for your help. I changed the commas in /dmri/bvecs to dots and reran trac-all. But the command xfmrot changed the dots back to commas. So, I changed our system language from de_AUT.UTF-8 to en_US.UTF-8 and reran trac-all. After changing the system language everything was genereted correctly and trac-all -prep ran without any errors. I'm so glad. Then, I started the next step trac-all -bedp and got a syntax error /usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: ( unexpected. I also attached the the logfile. I was reading about this error in the mail archive. Would I have to run bedpostx outside of tracula ? Sincerely, Florian Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 19.08.13 17.54 Uhr Hi Florian - Can you please change the decimal commas to points and try again? a.y On Mon, 19 Aug 2013, Borsodi Florian wrote: Hi Anastasia, Here are the bvec and bval files you asked me about. Sincerely, Florian Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 18.08.13 22.52 Uhr Hi Florian - Can you please also attach the bvecs/bvals files from the dmri directory? Thanks, a.y On Sun, 18 Aug 2013, Borsodi Florian wrote: Hi Anastasia, Thanks for your help. I renamed the directories and reran trac-all. It worked for the moment. However, then I got another error: bvecs and bvals don't have the same number of entries. I don't know why, because they actually have the same number of entries. I attached the logfile so that you may see what is going on. The error occours at line 1463. Thank you in advance for your help. Sincerely, Florian Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 15.08.13 18.01 Uhr Hi Florian - I see what's going on. Can you please rename the directory /data/physics/florian/nii into something that doesn't include nii, and rerun? Because nii is a file extension, this confuses some of the scripts. Thanks, a.y On Thu, 15 Aug 2013, Borsodi Florian wrote: Hi Anastasia I ran the command you sent me and it runs without any errors. I also attached the command line for you. Furthermore i ran data with 12 diffusion directions and i keep getting the same kind of problems. sincerely Florian Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 02.08.13 19.59 Uhr Hi Florian - Can you please run this command directly on the command line and see if there are any errors? flip4fsl /data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.nii.gz /data/physics/florian/nii/102485074_20080319/dmri/dwi_orig_flip.nii.gz Thanks, a.y On Fri, 2 Aug 2013, Borsodi Florian wrote: Hi Anastasia Thank you for your answer. Yes, those files exist. I also extracted the bvec an bval files with anotther software then dcm2nii and i keep getting the same kind of error. Also, about the 6 diffusion direction, those data i sent you, are just testdata for running tracula. sincerely Florian Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 02.08.13 0.41 Uhr Hi Florian - Do these files exist? /data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.mghdti.bvec s /data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.mghdti.bval s The format of the bvecs and bvals that you sent seems fine, but (and this has nothing to do with the error you're getting) I have to warn you that you may not be able to get good results running probabilistic tractography on this data. It looks like you're acquiring the same 6 diffusion directions, repeated 8 times. Six directions is the absolute minimum for reconstructing the tensor model, but will probably not be sufficient for the crossing fiber model that bedpostx reconstructs (and is used by tracula). Your scan time is better spent acquiring 48
Re: [Freesurfer] [Tracula] error running trac-all –path –c Configuration_file.txt
Hi Francesco - There's a list of bedpostx output files here: http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_bedpostx.html The best way to determine if bedpostx finished running properly is to check if those files were created in the dmri.bedpostX directory. a.y On Mon, 19 Aug 2013, Francesco Siciliano wrote: Hello, I received an error on several terminals running trac-all –path –c Configuration_file.txt 55 slices processed 56 slices processed 56 slices processed 57 slices processed 57 slices processed 58 slices processed 59 slices processed 60 slices processed 61 slices processed Queuing post processing stage 70 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. /Users/jonathanposner/Desktop/MRI_Software/FSL_installer/fsl/bin/bedpostx: line 262: kill: (15849) - No such process Is this an indication that the processing did not finish? Could this have anything to do with limited computer memory? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] [Tracula] error running trac-all –path –c Configuration_file.txt
Hi Francesco - The bedpostx files are created when you run trac-all -bedp. Then you need to run trac-all -path to reconstruct the paths under dpath/... as the final step. Did you run this? a.y On Mon, 19 Aug 2013, Francesco Siciliano wrote: Thank you! Is it normal, however, not to have a dpath folder with summary statistics? I have all of the bedpostx output files, however, I seem to be missing the dpath folder as well as a script confirming that -path was completed. Thanks, Francesco From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Monday, August 19, 2013 1:56 PM To: Francesco Siciliano Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [Tracula] error running trac-all –path –c Configuration_file.txt Hi Francesco - There's a list of bedpostx output files here: http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_bedpostx.html The best way to determine if bedpostx finished running properly is to check if those files were created in the dmri.bedpostX directory. a.y On Mon, 19 Aug 2013, Francesco Siciliano wrote: Hello, I received an error on several terminals running trac-all –path –c Configuration_file.txt 55 slices processed 56 slices processed 56 slices processed 57 slices processed 57 slices processed 58 slices processed 59 slices processed 60 slices processed 61 slices processed Queuing post processing stage 70 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. /Users/jonathanposner/Desktop/MRI_Software/FSL_installer/fsl/bin/bedpostx: line 262: kill: (15849) - No such process Is this an indication that the processing did not finish? Could this have anything to do with limited computer memory? The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] trac-all inquiry
Ok, actually the error about the data and bvals/bvecs not having the same size occured the first time you ran trac-all, but it seems to have been fixed the second time you ran it, based on the log file. I suspect the current problem is caused by poor registration. Have you checked the aparc+aseg and/or the registration from diffusion to anatomical and from anatomical to MNI? On Fri, 16 Aug 2013, David Soto wrote: hi - yes it as 65 -output pasted below, cheers dsoto@wmen-dsoto3:~/Documents/fmri/rsdtianawmgui/14AB/dmri$ mri_info dwi.nii.gz Volume information for dwi.nii.gz type: nii dimensions: 96 x 96 x 46 x 65 voxel sizes: 2., 2., 2.2999 type: FLOAT (3) fov: 224.000 dof: 0 xstart: -112.0, xend: 112.0 ystart: -112.0, yend: 112.0 zstart: -52.9, zend: 52.9 TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 65 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = 0. : x_a = 0., y_a = 0.9774, z_a = -0.2112, c_a = 2.1015 : x_s = 0., y_s = 0.2112, z_s = 0.9774, c_s = 19.9194 Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -2. 0. 0. 112. 0. 2.2807 -0.4858 -96.1994 0. 0.4928 2.2480 -55.4405 0. 0. 0. 1. voxel-to-ras determinant -12.5217 ras to voxel transform: -0.4286 0. 0.48. -0. 0.4189 0.090545.3166 -0. -0.0918 0.425014.7274 0. 0. 0. 1. http://www1.imperial.ac.uk/medicine/people/d.soto/ On 16/08/13 16:13, Anastasia Yendiki wrote: mri_info dmri/dwi.nii.gz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Trac Stats
Is it really autofs without the '/' in front? On Thu, 15 Aug 2013, Alan Francis wrote: Hi Anastasia: Sorry to bother you again. I am trying to extract trac stats from the FS data. When I run the following script, it gives me an error message: csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ recons] : tractstats2table --load-pathstats-from-file/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs/Forceps_Major_CC.list.txt --overall --tablefile/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs/Forceps_Major_CC.All.table Parsing the .stats files ERROR: The stats fileautofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_re cons/BW_101/dpath/fmajor_PP_avg33_mni_bbr/pathstats.overall.txt is not found or is too small to be a valid statsfile However, when I manually checked the pathstats.overall.txt, the data is physically there. Am I doing something wrong? thanks so much, Alan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Trac Stats
Can you please attach the file Forceps_Major_CC.list.txt? On Thu, 15 Aug 2013, Alan Francis wrote: Hi Anastasia: Yes the '/' is really there before the autofs. It is puzzling. thanks, Alan On Thu, Aug 15, 2013 at 3:15 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: I didn't suggest taking it off, I meant make sure that the '/' is there, because the error message suggested to me that a '/' was missing from a filename listed IN that text file. Check your original error message. On Thu, 15 Aug 2013, Alan Francis wrote: Hi Anastasia: I took off the '/' before the autofs, but then it gave me a different problem. csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5 .3_Data/diffusion_ recons] : tractstats2table--load-pathstats-from-fileautofs/space/dali_003/users/BW_project_DTI/FreeSu rfer_5.3_Data/diffusion_re cons/Forceps_Major_CC.list.txt --overall--tablefileautofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/d iffusion_re cons/Forceps_Major_CC.All.table ERROR: thefileautofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusio n_re cons/Forceps_Major_CC.list.txt doesnt exist Actually it does exist. thanks, Alan On Thu, Aug 15, 2013 at 2:40 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Is it really autofs without the '/' in front? On Thu, 15 Aug 2013, Alan Francis wrote: Hi Anastasia: Sorry to bother you again. I am trying to extract trac stats from the FS data. When I run the following script, it gives me an error message: csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5 .3_Data/diffusion_ recons] :tractstats2table--load-pathstats-from-file/autofs/space/dali_003/users/BW_p roject_DTI/FreeS urfer_5.3_Data/diffusion_r econs/Forceps_Major_CC.list.txt--overall--tablefile/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_ 5.3_Data/ diffusion_r econs/Forceps_Major_CC.All.table Parsing the .stats files ERROR: Thestatsfileautofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/dif fusio n_re cons/BW_101/dpath/fmajor_PP_avg33_mni_bbr/pathstats.overall.txt is not found or is too small to be a valid statsfile However, when I manually checked the pathstats.overall.txt, the data is physically there. Am I doing something wrong? thanks so much, Alan The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula failed
Hi Alan - I'm not sure where the output from the one subject ends the the other starts. For future reference, it's best to attach the entire trac-all.log files instead of copying and pasting parts of them into your message. I see two error messages here: 1. ERROR: must specify as many DWI dicoms as subjects This is as it says. Check your configuration file and see if the numbers of entries in subjlist and dcmlist are the same. 2. ERROR: reading /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_frame.nii.gz I'm guessing the problem is in the b-value table. How many entries are there that correspond to low-b images? a.y On Tue, 13 Aug 2013, Alan Francis wrote: Hi Anastasia: Thanks to your advice most of the data have been processed using Tracula. Two brains gave me error messages that are as follows: csh::alanf@cerebro [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all -prep -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-124 ERROR: must specify as many DWI dicoms as subjects csh::alanf@cerebro [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all -prep -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-118 INFO: SUBJECTS_DIR is /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons INFO: Diffusion root is /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/ Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 trac-preproc -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/dmrirc.local -log /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/trac-all.log -cmd /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/trac-all.cmd #- /usr/local/freesurfer/stable5_3_0//bin/trac-preproc #- #@# Image corrections Mon Aug 12 17:11:05 EDT 2013 mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/Diffusion_Recons/20090224_14110 2DIFFUSIONHighRess016a001.nii /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/Diffusion_Recons/20090224_14110 2DIFFUSIONHighRess016a001.nii /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/Diffusion_Recons/20090224_14110 2DIFFUSIONHighRess016a001.nii... TR=7640.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997762, -0.0667414, -0.00403802) j_ras = (-0.0662713, 0.979101, 0.192276) k_ras = (0.00887916, -0.192114, 0.981333) writing to /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz... cp /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/118/Diffusion_Recons/118.bvecs /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.mghdti.bvecs cp /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/118/Diffusion_Recons/118.bvals /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.mghdti.bvals flip4fsl /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -6.8719 fslswapdim /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz x y z /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.nii.gz INFO: found /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.mghdti.bvecs /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/bvecs mv
Re: [Freesurfer] trac-all download
Hi Ana - If you notice the release notes, this was relevant to an old version of tracula. You should now be using the latest version of tracula that's included in freesurfer 5.3, in which case you don't need any extra downloads. a.y On Wed, 14 Aug 2013, ana ;osp wrote: hi'm trying to download the trac-all file from the site in the tracula release notes, it is the download from 2012/1/09 recommended for all, but hen i click it open a page and gives me an errorshould i do something different than just click? thanks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula failed
Where did you get this command line? You should set the SUBJECTS_DIR to the location on disk where your freesurfer recons are. On Wed, 14 Aug 2013, Alan Francis wrote: Hi Anastasia: I fixed that problem - thank you. However, I have another question. i am trying extract trac data but when I set environment, I get an error message: csh::alanf@cerebro [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : setenv SUBJECTS_DIR $FreeSurfer_Data/diffusion_recons FreeSurfer_Data: Undefined variable. How do I solve this? Thanks again, Alan On Wed, Aug 14, 2013 at 11:06 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Alan - I'm not sure where the output from the one subject ends the the other starts. For future reference, it's best to attach the entire trac-all.log files instead of copying and pasting parts of them into your message. I see two error messages here: 1. ERROR: must specify as many DWI dicoms as subjects This is as it says. Check your configuration file and see if the numbers of entries in subjlist and dcmlist are the same. 2. ERROR: reading /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_frame.nii.gz I'm guessing the problem is in the b-value table. How many entries are there that correspond to low-b images? a.y On Tue, 13 Aug 2013, Alan Francis wrote: Hi Anastasia: Thanks to your advice most of the data have been processed using Tracula. Two brains gave me error messages that are as follows: csh::alanf@cerebro [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all -prep -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-124 ERROR: must specify as many DWI dicoms as subjects csh::alanf@cerebro [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all -prep -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-118 INFO: SUBJECTS_DIR is /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons INFO: Diffusion root is /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/ Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 trac-preproc -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/dmrirc.local -log /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/trac-all.log -cmd /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/trac-all.cmd #- /usr/local/freesurfer/stable5_3_0//bin/trac-preproc #- #@# Image corrections Mon Aug 12 17:11:05 EDT 2013 mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/Diffusion_Recons/200 90224_14110 2DIFFUSIONHighRess016a001.nii /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/Diffusion_Recons/200 90224_14110 2DIFFUSIONHighRess016a001.nii /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ readingfrom/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/Diffusion_Recons/20090224_1 4110 2DIFFUSIONHighRess016a001.nii... TR=7640.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997762, -0.0667414, -0.00403802) j_ras = (-0.0662713, 0.979101, 0.192276) k_ras = (0.00887916, -0.192114, 0.981333) writing to /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz... cp /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/118/Diffusion_Recons/118.bvecs /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.mghdti.bvecs cp /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/118/Diffusion_Recons/118.bvals /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.mghdti.bvals flip4fsl /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -6.8719 fslswapdim /autofs/space/dali_003/users/BW_project_DTI
Re: [Freesurfer] Tracula failed
Alan - Where is the location that has plenty of space? You should set your SUBJECTS_DIR to that location, e.g., setenv SUBJECTS_DIR /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons On Wed, 14 Aug 2013, Alan Francis wrote: Hi Anastasia/ FreeSurfers I did not use the conventional path usr/local/freesurfer. since there is very little disc space in this location. Alternately I set the environment at a location where is plenty of disc space and then sourced it. For the SUBJECTS_DIR I set the environment without using the dollar sign $. The Freesurfer recons and Tracula ran without problem and saved the processed data to this location. So the FReeSurfer recons and tracula data are in the same location. Now I am trying to use the dollar sign, so that I can extract the trac data, but I keep getting the error message. csh::alanf@cerebro [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : setenv SUBJECTS_DIR $FreeSurfer_Data/diffusion_recons FreeSurfer_Data: Undefined variable. thanks, Alan On Wed, Aug 14, 2013 at 1:08 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Where did you get this command line? You should set the SUBJECTS_DIR to the location on disk where your freesurfer recons are. On Wed, 14 Aug 2013, Alan Francis wrote: Hi Anastasia: I fixed that problem - thank you. However, I have another question. i am trying extract trac data but when I set environment, I get an error message: csh::alanf@cerebro [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : setenv SUBJECTS_DIR $FreeSurfer_Data/diffusion_recons FreeSurfer_Data: Undefined variable. How do I solve this? Thanks again, Alan On Wed, Aug 14, 2013 at 11:06 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Alan - I'm not sure where the output from the one subject ends the the other starts. For future reference, it's best to attach the entire trac-all.log files instead of copying and pasting parts of them into your message. I see two error messages here: 1. ERROR: must specify as many DWI dicoms as subjects This is as it says. Check your configuration file and see if the numbers of entries in subjlist and dcmlist are the same. 2. ERROR: reading /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_frame.nii.gz I'm guessing the problem is in the b-value table. How many entries are there that correspond to low-b images? a.y On Tue, 13 Aug 2013, Alan Francis wrote: Hi Anastasia: Thanks to your advice most of the data have been processed using Tracula. Two brains gave me error messages that are as follows: csh::alanf@cerebro [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all -prep -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-124 ERROR: must specify as many DWI dicoms as subjects csh::alanf@cerebro [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all -prep -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-118 INFO: SUBJECTS_DIR is /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons INFO: Diffusion root is /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/ Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 trac-preproc -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/dmrirc.local -log /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/trac-all.log -cmd /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/trac-all.cmd #- /usr/local/freesurfer/stable5_3_0//bin/trac-preproc #- #@# Image corrections Mon Aug 12 17:11:05 EDT 2013 mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/Diffusion_Recons/200 90224_14110 2DIFFUSIONHighRess016a001.nii /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz mri_convert/autofs/space
Re: [Freesurfer] Tracula failed
Why do you want to use a '$'? On Wed, 14 Aug 2013, Alan Francis wrote: Hi Anastasia: Yes the path that you pointed out is the one I presently use. Is there no way to use the '$' as a substitute? thanks, Alan On Wed, Aug 14, 2013 at 1:46 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Alan - Where is the location that has plenty of space? You should set your SUBJECTS_DIR to that location, e.g., setenv SUBJECTS_DIR /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons On Wed, 14 Aug 2013, Alan Francis wrote: Hi Anastasia/ FreeSurfers I did not use the conventional path usr/local/freesurfer. since there is very little disc space in this location. Alternately I set the environment at a location where is plenty of disc space and then sourced it. For the SUBJECTS_DIR I set the environment without using the dollar sign $. The Freesurfer recons and Tracula ran without problem and saved the processed data to this location. So the FReeSurfer recons and tracula data are in the same location. Now I am trying to use the dollar sign, so that I can extract the trac data, but I keep getting the error message. csh::alanf@cerebro [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : setenv SUBJECTS_DIR $FreeSurfer_Data/diffusion_recons FreeSurfer_Data: Undefined variable. thanks, Alan On Wed, Aug 14, 2013 at 1:08 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Where did you get this command line? You should set the SUBJECTS_DIR to the location on disk where your freesurfer recons are. On Wed, 14 Aug 2013, Alan Francis wrote: Hi Anastasia: I fixed that problem - thank you. However, I have another question. i am trying extract trac data but when I set environment, I get an error message: csh::alanf@cerebro [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : setenv SUBJECTS_DIR $FreeSurfer_Data/diffusion_recons FreeSurfer_Data: Undefined variable. How do I solve this? Thanks again, Alan On Wed, Aug 14, 2013 at 11:06 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Alan - I'm not sure where the output from the one subject ends the the other starts. For future reference, it's best to attach the entire trac-all.log files instead of copying and pasting parts of them into your message. I see two error messages here: 1. ERROR: must specify as many DWI dicoms as subjects This is as it says. Check your configuration file and see if the numbers of entries in subjlist and dcmlist are the same. 2. ERROR: reading /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_frame.nii.gz I'm guessing the problem is in the b-value table. How many entries are there that correspond to low-b images? a.y On Tue, 13 Aug 2013, Alan Francis wrote: Hi Anastasia: Thanks to your advice most of the data have been processed using Tracula. Two brains gave me error messages that are as follows: csh::alanf@cerebro [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all -prep -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-124 ERROR: must specify as many DWI dicoms as subjects csh::alanf@cerebro [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all -prep -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-118 INFO: SUBJECTS_DIR is /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons INFO: Diffusion root is /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/ Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 trac-preproc -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/dmrirc.local -log /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/trac-all.log -cmd /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/trac-all.cmd #- /usr/local/freesurfer/stable5_3_0//bin/trac-preproc
Re: [Freesurfer] trac-all download
If you already have the 5.1 version and have used it on some subjects, you can of course use the same version on the other subjects. But if you're going to download something new, that should be the 5.3 version, not an intermediate update to 5.1. It's highly recommended to use the 5.3 version of tracula b/c there are several improvements to it. On Wed, 14 Aug 2013, ana ;osp wrote: thanksbut i'have all the data processed with 5.1 and i still have a few subjects to process so i didn't want to download the 5.3 and mix versions... is there anyway to have it without download the 5.3? thanks On Wed, Aug 14, 2013 at 11:11 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ana - If you notice the release notes, this was relevant to an old version of tracula. You should now be using the latest version of tracula that's included in freesurfer 5.3, in which case you don't need any extra downloads. a.y On Wed, 14 Aug 2013, ana ;osp wrote: hi'm trying to download the trac-all file from the site in the tracula release notes, it is the download from 2012/1/09 recommended for all, but hen i click it open a page and gives me an errorshould i do something different than just click? thanks The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Preproc
Hi Alan - This appears to be the same error message as the one for subject 118 that you sent yesterday. So I'd try here whatever you did to fix that one. a.y On Wed, 14 Aug 2013, Alan Francis wrote: Hi Anastasia: Sorry to bother you again. Another of my brains gave an error message. I have enclosed the trac-all log as an attachment. Thanks ever so much for your help, Alan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] trac-all inquiry
When you apply a rotation to the DWIs (as eddy_correct does), you need to apply the same rotation to the corresponding gradient vectors. See for example: Leemans, A., Jones, D. K., Jun 2009. The B-matrix must be rotated when correcting for subject motion in DTI data. Magn Reson Med 61 (6), 1336–49. If you don't want to pass the dicoms to trac-all directly, you can use mri_convert to convert from dicom to nifti. On Fri, 9 Aug 2013, Soto, David wrote: hi - am afraid not because I am feeding to trac-all already eddycorrected images then in the config file I have # Perform registration-based eddy-current compensation? # Default: 1 (yes) set doeddy = 0 # Rotate diffusion gradient vectors to match eddy-current compensation? # Only used if doeddy = 1 # Default: 1 (yes) is this critical?? unfortunately, this is the only way I manage to get it to work as said my diffusion outputs from mriconverter are not read by FS, only through mediation of some FSL operation on the files, then FS likes those. I could start from scratch using dicoms but would prefer not to as the data is already well organised cheers ds http://www1.imperial.ac.uk/medicine/people/d.soto/ From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: 09 August 2013 22:44 To: Soto, David Subject: Re: [Freesurfer] trac-all inquiry Are you rotating the gradient vectors accordingly? This is done in trac-all after running eddy_correct. On Fri, 9 Aug 2013, Soto, David wrote: Hi Anastasia, stuff is running smoothly at last one quick question, is there any 'disadvantage' in using FSL to do the eddy correct and then feed those images to trace-all ? cheers ds http://www1.imperial.ac.uk/medicine/people/d.soto/ On 9 Aug 2013, at 15:33, David Soto ds...@imperial.ac.uk wrote: hi, for some reason FS does not like the nii file from Mriconverter, ( I saw a post about this http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19526.html ) but does like the nii.gz outputs from FSL... I'll try to debug the bepostx error thanks! ds http://www1.imperial.ac.uk/medicine/people/d.soto/ On 09/08/13 14:26, Anastasia Yendiki wrote: There is no reason to conevrt to .mnc. You should use your original .nii, if that shows up correctly in freeview. As for the bedpostx error, this is an Ubuntu issue that has come to my attention very recently. In Ubuntu /bin/sh is not a bash shell any more. To get around this, you'll have to edit the first line of the scripts $FREESURFER_HOME/bin/bedpostx_mgh and $FREESURFER_HOME/bin/fsl_sub_mgh. You'll have to replace /bin/sh with /bin/bash on the first line of those two scripts. On Fri, 9 Aug 2013, David Soto wrote: hi- I tried to convert from nii to mnc becos that is what i did when I did recon-all but I also tried with nii at the beggining and got the same issues. In fact in my last post (pasted below again)the input was a nii file could you please check the stuff below? thanks! ds Hi, further to my prior email I made some progress. I noted that nii2mnc does not seem to work on the diffusion output.nii that I got from Mriconverter as the output.mnc brain has parts chopped in Freeview. (I think there may be something funny about this, as the recon-all does like the T1 output form Mriconverter) HENCE I tried use the output of eddycorrect from FSL (which I already run for other thing) Then I created a new folder where i placed the output of FSL eddycorrect and in the configuration file I did (i) set dcmlist = (fsleddycorrectoutput.nii.gz) (ii) turned 'set doeddy = 0' then run it trac-all -c traculatest.txt -prep -log trac_from_fsleddy it seemed to complete without errors (log attached)n and I checked the preprocessing outputs in Freeview (FA, masks and aparc+asegs) and all seemed fine. However when I attempt the next stage in trac-all i.e. trac-all -c traculatest.txt -bedp -log trac_from_fsleddy_bedp it fails saying the following /usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: ( unexpected the log is also attached. any advise appreciated! cheers ds http://www1.imperial.ac.uk/medicine/people/d.soto/ http://www1.imperial.ac.uk/medicine/people/d.soto/ On 09/08/13 14:02, Anastasia Yendiki wrote
Re: [Freesurfer] trac-all inquiry
I didn't mean run mri_convert on the nifti output of another program. I meant run mri_convert directly on the original dicom to convert it to nifti: mri_convert yourimage.dcm yourimage.nii.gz On Fri, 9 Aug 2013, Soto, David wrote: I see - as said the diffusion output.nii from MRIConverter http://lcni.uoregon.edu/~jolinda/MRIConvert/ [to not confound it with mri_converter) is not read by Freeview and mri_converter does not like it either --- MD00071523-2:RSDTI_WMGUI/ACH_AMO/diff] dsoto% mri_convert output.nii data.mgz mri_convert output.nii data.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from output.nii... nifti1Read(): unsupported slice timing pattern 5 in /Users/dsoto/Documents/fMRI/RSDTI_WMGUI/ACH_AMO/diff/output.nii No such file or directory --- NOW, I find that if I use FSL and run bet with a fractional intensity threshold of 0, I get an output file which is read by Freeview- which should allow me to proceed with all the necessary preprocessing steps in trac-all would this be fine? I dont think the bet I run will affect the image cheers ds http://www1.imperial.ac.uk/medicine/people/d.soto/ From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: 09 August 2013 23:15 To: Soto, David Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] trac-all inquiry When you apply a rotation to the DWIs (as eddy_correct does), you need to apply the same rotation to the corresponding gradient vectors. See for example: Leemans, A., Jones, D. K., Jun 2009. The B-matrix must be rotated when correcting for subject motion in DTI data. Magn Reson Med 61 (6), 1336–49. If you don't want to pass the dicoms to trac-all directly, you can use mri_convert to convert from dicom to nifti. On Fri, 9 Aug 2013, Soto, David wrote: hi - am afraid not because I am feeding to trac-all already eddycorrected images then in the config file I have # Perform registration-based eddy-current compensation? # Default: 1 (yes) set doeddy = 0 # Rotate diffusion gradient vectors to match eddy-current compensation? # Only used if doeddy = 1 # Default: 1 (yes) is this critical?? unfortunately, this is the only way I manage to get it to work as said my diffusion outputs from mriconverter are not read by FS, only through mediation of some FSL operation on the files, then FS likes those. I could start from scratch using dicoms but would prefer not to as the data is already well organised cheers ds http://www1.imperial.ac.uk/medicine/people/d.soto/ From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: 09 August 2013 22:44 To: Soto, David Subject: Re: [Freesurfer] trac-all inquiry Are you rotating the gradient vectors accordingly? This is done in trac-all after running eddy_correct. On Fri, 9 Aug 2013, Soto, David wrote: Hi Anastasia, stuff is running smoothly at last one quick question, is there any 'disadvantage' in using FSL to do the eddy correct and then feed those images to trace-all ? cheers ds http://www1.imperial.ac.uk/medicine/people/d.soto/ On 9 Aug 2013, at 15:33, David Soto ds...@imperial.ac.uk wrote: hi, for some reason FS does not like the nii file from Mriconverter, ( I saw a post about this http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19526.html ) but does like the nii.gz outputs from FSL... I'll try to debug the bepostx error thanks! ds http://www1.imperial.ac.uk/medicine/people/d.soto/ On 09/08/13 14:26, Anastasia Yendiki wrote: There is no reason to conevrt to .mnc. You should use your original .nii, if that shows up correctly in freeview. As for the bedpostx error, this is an Ubuntu issue that has come to my attention very recently. In Ubuntu /bin/sh is not a bash shell any more. To get around this, you'll have to edit the first line of the scripts $FREESURFER_HOME/bin/bedpostx_mgh and $FREESURFER_HOME/bin/fsl_sub_mgh. You'll have to replace /bin/sh with /bin/bash on the first line of those two scripts. On Fri, 9 Aug 2013, David Soto wrote: hi- I tried to convert from nii to mnc becos that is what i did when I did recon-all but I also tried with nii at the beggining and got the same issues. In fact in my last post (pasted below again)the input was a nii file could you please check the stuff below? thanks! ds Hi, further to my prior email I made some progress. I noted that nii2mnc does not seem to work on the diffusion output.nii that I got from Mriconverter as the output.mnc brain
Re: [Freesurfer] trac-all inquiry
Hi David - The fact that it's taking so many tries to initialize the left ILF tells me that something has gone wrong with the data, either with the T1 to DWI registration, or with the mask, or something like that. Have you looked at any of the output files of the pre-processing? The FA map, the aparc+aseg, etc? a.y On Wed, 7 Aug 2013, Soto, David wrote: Hi Anastasia, I checked the becs and bvals files, there was a bug in the transposition of the columns into 3 rows in the bvecs. But i still have problems.. I rerun trac-all -prep and seemed fine but ended with a Segmentation fault (core dumped) which however is not present in the last line of the trac-all.log (Attached). Writing output files to /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_* Writing spline volume to /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_cpts_5.nii.gz Segmentation fault (core dumped) Just in case I tried trac-all -bedp complains like these below, any advise appreciated, cheers - ds /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/diffree/tracula02ST.txt -bedp INFO: SUBJECTS_DIR is /home/dsoto/Documents/fmri/rsdtianawmgui INFO: Diffusion root is /home/dsoto/Documents/fmri/rsdtianawmgui Actual FREESURFER_HOME /usr/local/freesurfer WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri /usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: ( unexpected http://www1.imperial.ac.uk/medicine/people/d.soto/ From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: 07 August 2013 17:22 To: Soto, David Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] trac-all inquiry Hi David - Every time you run trac-all, the results get appended to this file, so you need to look for error messages only in the more recent invocation of trac-all. The first error there seems to be: Error: bvecs and bvals don't have the same number of entries Do you have the same number of b-values and gradient vectors and volumes in your DWI series? a.y On Tue, 6 Aug 2013, Soto, David wrote: hi I upgraded to FS 5.3 but still encountering issues with trac-all prep. The log is attached, things I noted after inspecting it 1) INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 2) Error: input image /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb not valid 3) Image Exception : #22 :: ERROR: Could not open image /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb_brain 4) Image Exception : #22 :: ERROR: Could not open image /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/White-Matter++. 5) ERROR: Could not read /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dtifit_FA.nii.gz but despite all this it says: trac-preproc finished without error at Tue Aug 6 21:27:30 BST 2013 thanks for your help cheers ds http://www1.imperial.ac.uk/medicine/people/d.soto/ From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: 06 August 2013 19:30 To: Soto, David Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] trac-all inquiry I see, you're using the old version of tracula (from freesurfer 5.1). In that version, you had to define the number of low-b images in the configuration file. I strongly recommend updating to freesurfer 5.3. A lot of things have improved in tracula since then. Also, in the future please attach any log files as separate attachments instead of pasting them into the body of your email - this causes the body of the email to exceed the limit allowable on the list. Thanks, a.y The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] trac-all inquiry
Hi David - Every time you run trac-all, the results get appended to this file, so you need to look for error messages only in the more recent invocation of trac-all. The first error there seems to be: Error: bvecs and bvals don't have the same number of entries Do you have the same number of b-values and gradient vectors and volumes in your DWI series? a.y On Tue, 6 Aug 2013, Soto, David wrote: hi I upgraded to FS 5.3 but still encountering issues with trac-all prep. The log is attached, things I noted after inspecting it 1) INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 2) Error: input image /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb not valid 3) Image Exception : #22 :: ERROR: Could not open image /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb_brain 4) Image Exception : #22 :: ERROR: Could not open image /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/White-Matter++. 5) ERROR: Could not read /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dtifit_FA.nii.gz but despite all this it says: trac-preproc finished without error at Tue Aug 6 21:27:30 BST 2013 thanks for your help cheers ds http://www1.imperial.ac.uk/medicine/people/d.soto/ From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: 06 August 2013 19:30 To: Soto, David Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] trac-all inquiry I see, you're using the old version of tracula (from freesurfer 5.1). In that version, you had to define the number of low-b images in the configuration file. I strongly recommend updating to freesurfer 5.3. A lot of things have improved in tracula since then. Also, in the future please attach any log files as separate attachments instead of pasting them into the body of your email - this causes the body of the email to exceed the limit allowable on the list. Thanks, a.y The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula question
Yes, please attach the dmrirc and trac-all.log. Thanks! a.y On Wed, 7 Aug 2013, Alan Francis wrote: Hi Anastasia: For one brain I got this error message : csh::alanf@cerebro [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all -prep -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-107 Too many ('s. ERROR: must specify as many DWI dicoms as subjects I tried specifying the exact number of DWI dicoms but it is not working. Should I send you my dmrirc for this brain? thanks, Alan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula question
Please attach the file trac-all.log. I can't tell what's going on just by looking at the end of it. On Wed, 7 Aug 2013, Alan Francis wrote: Thank you Anastasia. Another brain had a different problem: Here is the trac-all log: mri_concat --i /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_frame.nii.gz --mean --o /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/lowb.nii.gz niiRead(): error opening file /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_frame.nii.gz Linux cerebro 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Aug 7 13:01:21 EDT 2013 thanks so much, Alan On Wed, Aug 7, 2013 at 1:11 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Alan - Try removing the \ character from the end of the dcmlist definition. That's a change of line character. a.y On Wed, 7 Aug 2013, Alan Francis wrote: Hi Anastasia: Here is the trac-all log. Please find attached the dmrirc file. csh::alanf@cerebro [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all -prep -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-107 Too many ('s. ERROR: must specify as many DWI dicoms as subjects Thank you so much. Alan On Wed, Aug 7, 2013 at 12:32 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Yes, please attach the dmrirc and trac-all.log. Thanks! a.y On Wed, 7 Aug 2013, Alan Francis wrote: Hi Anastasia: For one brain I got this error message : csh::alanf@cerebro [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all -prep -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-107 Too many ('s. ERROR: must specify as many DWI dicoms as subjects I tried specifying the exact number of DWI dicoms but it is not working. Should I send you my dmrirc for this brain? thanks, Alan The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula question
/diffusion_recons//106/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_frame.nii.gz Linux cerebro 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Aug 7 13:34:45 EDT 2013 On Wed, Aug 7, 2013 at 1:20 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Please attach the file trac-all.log. I can't tell what's going on just by looking at the end of it. On Wed, 7 Aug 2013, Alan Francis wrote: Thank you Anastasia. Another brain had a different problem: Here is the trac-all log: mri_concat --i /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_frame.nii.gz --mean --o /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/lowb.nii.gz niiRead(): error opening file /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_frame.nii.gz Linux cerebro 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Aug 7 13:01:21 EDT 2013 thanks so much, Alan On Wed, Aug 7, 2013 at 1:11 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Alan - Try removing the \ character from the end of the dcmlist definition. That's a change of line character. a.y On Wed, 7 Aug 2013, Alan Francis wrote: Hi Anastasia: Here is the trac-all log. Please find attached the dmrirc file. csh::alanf@cerebro [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all -prep -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-107 Too many ('s. ERROR: must specify as many DWI dicoms as subjects Thank you so much. Alan On Wed, Aug 7, 2013 at 12:32 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Yes, please attach the dmrirc and trac-all.log. Thanks! a.y On Wed, 7 Aug 2013, Alan Francis wrote: Hi Anastasia: For one brain I got this error message : csh::alanf@cerebro [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all -prep -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-107 Too many ('s. ERROR: must specify as many DWI dicoms as subjects I tried specifying the exact number of DWI dicoms but it is not working. Should I send you my dmrirc for this brain? thanks, Alan The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you
Re: [Freesurfer] preferred method for generating appropriate bvecs for tracula
set x = `cat bvecs | awk '{if (NR==1) print}'` set y = `cat bvecs | awk '{if (NR==2) print}'` set z = `cat bvecs | awk '{if (NR==3) print}'` @ k = 1 while ( $k = `head -1 bvecs|wc -w` ) echo $x[$k] $y[$k] $z[$k] @ k = $k + 1 end I'd make sure though dcm2nii doesn't L-R flip the gradient vectors, I think there was a thread recently that suggested it might. On Wed, 7 Aug 2013, Salil Soman wrote: Hi, I have dicoms that I turn to nifti using dcm2nii (with the default settings plus anonymization option turned on [-a y]). The bvec files it generates by default are 3 rows by n columns (where n is b0 number + directions). I am under the impression tracula requires this to be converted to a n row by 3 column file. 1) is this correct, 2) is there a preferred way to perform this transformation on linux systems? Thanks you, -Sal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] preferred method for generating appropriate bvecs for tracula
Hi Sal - Right now you'd just have to try it on one data set and look at the eigenvectors of the tensor (display dmri/dtifit_V1.nii.gz as lines) to make sure they're pointing in the right way. I'm hoping for the next freesurfer release to finally get mri_convert to read gradient vectors off the dicom header in a way that ends this gradient flipping madness once and for all. But for now you just have to check before you proceed, sorry! a.y On Wed, 7 Aug 2013, Salil Soman wrote: Thank you for the email. I saw a warning to check for flipping L-R from the dcm2nii site: http://www.mccauslandcenter.sc.edu/mricro/mricron/dcm2nii.html Is the problem you mentioned vendor specific (I have all GE data). Is there a different tool you would recommend for generating the bvec files? I would prefer to run tracula right off the original dicom images but transferring them to the cluster and anonymizing them would be prohibitively difficult. I could not find the freesurfer archive message you referred to. Any pointers would be greatly appreciated. Best wishes, Sal On Wed, Aug 7, 2013 at 1:12 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: set x = `cat bvecs | awk '{if (NR==1) print}'` set y = `cat bvecs | awk '{if (NR==2) print}'` set z = `cat bvecs | awk '{if (NR==3) print}'` @ k = 1 while ( $k = `head -1 bvecs|wc -w` ) echo $x[$k] $y[$k] $z[$k] @ k = $k + 1 end I'd make sure though dcm2nii doesn't L-R flip the gradient vectors, I think there was a thread recently that suggested it might. On Wed, 7 Aug 2013, Salil Soman wrote: Hi, I have dicoms that I turn to nifti using dcm2nii (with the default settings plus anonymization option turned on [-a y]). The bvec files it generates by default are 3 rows by n columns (where n is b0 number + directions). I am under the impression tracula requires this to be converted to a n row by 3 column file. 1) is this correct, 2) is there a preferred way to perform this transformation on linux systems? Thanks you, -Sal The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] preferred method for generating appropriate bvecs for tracula
Freeview can do this in principle, but the current version of freeview has a known bug with displaying eigenvectors as lines (see known issues in http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes), so for now you can use fslview. On Wed, 7 Aug 2013, Salil Soman wrote: Thank you for your response. Is there a best way to review the eigenvectors (tkmedit, freeview, other program?). Thank you. -S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] trac-preproc
You're welcome. It seems like it can't find this file: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data//bin/dmri_train I can't tell exactly what's going on without looking at your trac-all.log in its entirety. Can you please send it? On Tue, 6 Aug 2013, Alan Francis wrote: Thank you. It worked. I have been running a few brains and they have been preprocessed successfully. One brain gave me an error message. Can you please help me address this: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data//bin/dmri_train: Command not found. Linux cerebro 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Tue Aug 6 10:22:18 EDT 2013 Thanks so much, Alan On Mon, Aug 5, 2013 at 3:55 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Alan - The file doesn't need to have an extension, .txt or other. But you do need to set bvecfile to the full name of the file, including the extension, if it has one. a.y On Mon, 5 Aug 2013, Alan Francis wrote: Hi Anastasia: Yes this file does exist but it did not have the *.txt suffix. Maybe I will change the suffix and run this again. thanks, Alan On Mon, Aug 5, 2013 at 1:57 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: The error says: `/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ recons/bvecs.txt': No such file or directory Does this file exist? On Mon, 5 Aug 2013, Alan Francis wrote: Hi All: When I ran trac-preproc I got an error that read s as follows: trac-preproc exited with ERRORS at Mon Aug 5 13:12:53 EDT 2013. I do have a bvec.txt and bval file in each directory. thanks for your help, Alan The following are the messages: csh::alanf@cerebro [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data] : trac-all -prep -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs/dmrirc INFO: SUBJECTS_DIR is/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs INFO: Diffusion root is/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs/ Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 trac-preproc -c/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs//BW_101/scripts/dmrirc.local -log /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs//BW_101/scripts/trac-all.log -cmd /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs//BW_101/scripts/trac-all.cmd #- /usr/local/freesurfer/stable5_3_0//bin/trac-preproc #- #@# Image corrections Mon Aug 5 13:12:10 EDT 2013 mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs//BW_101/Diffusion_Recons/20080424_182054563000-12-01DTIValera s012a001.nii /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs//BW_101/dmri/dwi_orig.nii.gz mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs//BW_101/Diffusion_Recons/20080424_182054563000-12-01DTIValera s012a001.nii /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs//BW_101/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs//BW_101/Diffusion_Recons/20080424_182054563000-12-01DTIValera s012a001.nii... TR=7570.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.989696, 0.0161603, 0.142271) j_ras = (0.0163, 0.999867, -0.000183368) k_ras = (0.142255, -0.00213754, 0.989828) writing to/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs//BW_101/dmri/dwi_orig.nii.gz... cp/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs/bvecs.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
Re: [Freesurfer] trac-all inquiry
I see, you're using the old version of tracula (from freesurfer 5.1). In that version, you had to define the number of low-b images in the configuration file. I strongly recommend updating to freesurfer 5.3. A lot of things have improved in tracula since then. Also, in the future please attach any log files as separate attachments instead of pasting them into the body of your email - this causes the body of the email to exceed the limit allowable on the list. Thanks, a.y ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Trac-all question
Hi Alan - On the tutorial page you need to follow the directions under If you are not at an organized course, and $TUTORIAL_DATA is whatever directory you have downloaded the tutorial data in. Please address questions to the list and not to me personally, as other people may have the same issue and this way the answers get archived. Thanks, a.y On Mon, 5 Aug 2013, Alan Francis wrote: Hi Anastasia: Sorry about being a pest. One more question. I am running the Tutorial data to get a better understanding of Tracula. When I type $TUTORIAL_DATA, it keeps saying Undefined variable. Could you please help me. Thanks, Alan csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D ATA/diffusion_recons] : setenv FREESURFER_HOME /usr/local/freesurfer/stable5_3_0/ csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D ATA/diffusion_recons] : source $FREESURFER_HOME/Set SetUpFreeSurfer.csh* SetUpFreeSurfer.sh* csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D ATA/diffusion_recons] : source $FREESURFER_HOME/SetUpFreeSurfer.csh freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/stable5_3_0/ FSFAST_HOME /usr/local/freesurfer/stable5_3_0//fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/stable5_3_0//subjects MNI_DIR /usr/local/freesurfer/stable5_3_0//mni FSL_DIR /usr/pubsw/packages/fsl/current csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D ATA/diffusion_recons] : setenv SUBJECTS_DIR $TUTORIAL_DATA/d $TUTORIAL_DATA/ not found csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D ATA/diffusion_recons] : setenv SUBJECTS_DIR /autofs/space/d dali_001/ dali_002/ dali_003/ csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D ATA/diffusion_recons] : setenv SUBJECTS_DIR/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_DA TA/diffusion_recons/ csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D ATA/diffusion_recons] : gedit $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial TUTORIAL_DATA: Undefined variable. csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D ATA/diffusion_recons] : gedit /TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial [1] 32742 csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D ATA/diffusion_recons] : trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial TUTORIAL_DATA: Undefined variable. On Fri, Aug 2, 2013 at 7:16 PM, Alan Francis alandarkene...@gmail.com wrote: thanks again. On Fri, Aug 2, 2013 at 3:51 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: It can have any name you want. You just have to type the right name next to the -c ... On Fri, 2 Aug 2013, Alan Francis wrote: Sorry. I have another question. Should I name the config file dmrirc.txt or is there any other name? thank you so much, Alan On Fri, Aug 2, 2013 at 2:45 PM, Alan Francis alandarkene...@gmail.com wrote: Thanks Anastasia. On Fri, Aug 2, 2013 at 2:26 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Alan - All the set ... commands for tracula need to be in a configuration file. You then pass that configuration file as an argument to the -c option of trac-all. See tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Hope this helps, a.y On Fri, 2 Aug 2013, Alan Francis wrote: Hi Anastasia and others: I have been trying to run Trac all on five brains. It keeps giving me the error message: ERROR: run list is longer than subject list My run list is equal to the subject list: Here is the environment: Thanks for your help, Alan Martinos Center for Biomedical Imaging __ freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 Setting up environment for FreeSurfer/FS-FAST (and FSL
Re: [Freesurfer] trac-preproc
The error says: `/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/bvecs.txt': No such file or directory Does this file exist? On Mon, 5 Aug 2013, Alan Francis wrote: Hi All: When I ran trac-preproc I got an error that read s as follows: trac-preproc exited with ERRORS at Mon Aug 5 13:12:53 EDT 2013. I do have a bvec.txt and bval file in each directory. thanks for your help, Alan The following are the messages: csh::alanf@cerebro [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data] : trac-all -prep -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc INFO: SUBJECTS_DIR is /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons INFO: Diffusion root is /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/ Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 trac-preproc -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/scripts/dmrirc.local -log /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/scripts/trac-all.log -cmd /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/scripts/trac-all.cmd #- /usr/local/freesurfer/stable5_3_0//bin/trac-preproc #- #@# Image corrections Mon Aug 5 13:12:10 EDT 2013 mri_convert /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/Diffusion_Recons/20080424_182054563000-12-01DTIValeras012a001.nii /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/dmri/dwi_orig.nii.gz mri_convert /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/Diffusion_Recons/20080424_182054563000-12-01DTIValeras012a001.nii /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/Diffusion_Recons/20080424_182054563000-12-01DTIValeras012a001.nii... TR=7570.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.989696, 0.0161603, 0.142271) j_ras = (0.0163, 0.999867, -0.000183368) k_ras = (0.142255, -0.00213754, 0.989828) writing to /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/dmri/dwi_orig.nii.gz... cp /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/bvecs.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/dmri/dwi_orig.mghdti.bvecs cp: cannot stat `/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/bvecs.txt': No such file or directory Linux cerebro 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Mon Aug 5 13:12:53 EDT 2013 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] trac-preproc
Hi Alan - The file doesn't need to have an extension, .txt or other. But you do need to set bvecfile to the full name of the file, including the extension, if it has one. a.y On Mon, 5 Aug 2013, Alan Francis wrote: Hi Anastasia: Yes this file does exist but it did not have the *.txt suffix. Maybe I will change the suffix and run this again. thanks, Alan On Mon, Aug 5, 2013 at 1:57 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: The error says: `/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ recons/bvecs.txt': No such file or directory Does this file exist? On Mon, 5 Aug 2013, Alan Francis wrote: Hi All: When I ran trac-preproc I got an error that read s as follows: trac-preproc exited with ERRORS at Mon Aug 5 13:12:53 EDT 2013. I do have a bvec.txt and bval file in each directory. thanks for your help, Alan The following are the messages: csh::alanf@cerebro [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data] : trac-all -prep -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs/dmrirc INFO: SUBJECTS_DIR is/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs INFO: Diffusion root is/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs/ Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 trac-preproc -c/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs//BW_101/scripts/dmrirc.local -log /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs//BW_101/scripts/trac-all.log -cmd /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs//BW_101/scripts/trac-all.cmd #- /usr/local/freesurfer/stable5_3_0//bin/trac-preproc #- #@# Image corrections Mon Aug 5 13:12:10 EDT 2013 mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs//BW_101/Diffusion_Recons/20080424_182054563000-12-01DTIValera s012a001.nii /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs//BW_101/dmri/dwi_orig.nii.gz mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs//BW_101/Diffusion_Recons/20080424_182054563000-12-01DTIValera s012a001.nii /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs//BW_101/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs//BW_101/Diffusion_Recons/20080424_182054563000-12-01DTIValera s012a001.nii... TR=7570.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.989696, 0.0161603, 0.142271) j_ras = (0.0163, 0.999867, -0.000183368) k_ras = (0.142255, -0.00213754, 0.989828) writing to/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs//BW_101/dmri/dwi_orig.nii.gz... cp/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs/bvecs.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs//BW_101/dmri/dwi_orig.mghdti.bvecs cp: cannot stat`/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ recons/bvecs.txt': No such file or directory Linux cerebro 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Mon Aug 5 13:12:53 EDT 2013 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] trac-all inquiry
Hi David - You need to run each of the steps (-prep, -bedp, -path) separately. You can't run them all at the same time. See tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula Hope this helps, a.y On Fri, 2 Aug 2013, David Soto wrote: Hi, I have successfully run recon-all in my dataset and now am attempting to use trac-all on my diffusion data obtained on a Siemens scanner. Diffusion dicoms were transformed to .nii using MRIConverter and then to .mnc using nii2mnc output.nii output_t.mnc. I am trying to run trac-all on a single subject and for this I have created the configuration file attached (tracula02ST) As you can see the SUBJECTS_DIR is /home/dsoto/Documents/fmri/rsdtianawmgui and within each subject the T1 serving as input for recon-all are in mri/orig while the diffusion images are in a folder call diffdata (named output_t.mnc) which also contains the bvecs and bvals files, which were transposed and organised according to the tutorial (named as bvecs_t.txt and bvals_t.txt) When I run: trac-all -c tracula02ST.txt I get: ERROR: no analysis step (-{prep,bedp,path}) has been selected THEN I run: trac-all -prep -bedp -path -c tracula02ST.txt which runs for 5 seconds or so and then gives the long output text below with an error message. Segmentation fault (core dumped) foreach: No match. The trac-all.log is attached also. Could you please help? Cheers David ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Trac-all question
Hi Alan - All the set ... commands for tracula need to be in a configuration file. You then pass that configuration file as an argument to the -c option of trac-all. See tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Hope this helps, a.y On Fri, 2 Aug 2013, Alan Francis wrote: Hi Anastasia and others: I have been trying to run Trac all on five brains. It keeps giving me the error message: ERROR: run list is longer than subject list My run list is equal to the subject list: Here is the environment: Thanks for your help, Alan Martinos Center for Biomedical Imaging __ freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/stable5_3_0/ FSFAST_HOME /usr/local/freesurfer/stable5_3_0//fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/stable5_3_0//subjects MNI_DIR /usr/local/freesurfer/stable5_3_0//mni FSL_DIR /usr/pubsw/packages/fsl/current csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ recons] : setenv SUBJECTS_DIR /autofs/space/d dali_001/ dali_002/ dali_003/ csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ recons] : setenv SUBJECTS_DIR/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs/ csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ recons] : set dtroot = /autofs/space/d dali_001/ dali_002/ dali_003/ csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ recons] : set dtroot =/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs/ csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ recons] : set subjlist = (101/ 102/ 103/ 104/ 105/) csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ recons] : set dcmroot = /autofs/space/d dali_001/ dali_002/ dali_003/ csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ recons] : set dcmroot =/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs/ csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ recons] : set dcmlist =(101/Diffusion_Recons/20080424_182054563000-12-01DTIValeras012a001. nii \ ?102/Diffusion_Recons/20080911_101015358000-10-01DIFFUSIONHighResval erabi1002s010a001.nii \ ?103/Diffusion_Recons/20080911_140753578000-10-01DIFFUSIONHighResval eraBI1003s010a001.nii \ ?104/Diffusion_Recons/20080915_160812745000-10-01DIFFUSIONHighResVal eraBI104s010a001.nii \ ?105/Diffusion_Recons/20080917_190940899000-16-01DIFFUSIONHighResVal eraBI105s016a001.nii \ ? ) csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ recons] : set runlist = (101/ 102/ 103/ 104/ bem/ mri/ stats/ touch/ Diffusion_Recons/ scripts/ surf/ trash/ label/ src/ tmp/ csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ recons] : set runlist = (101/ 102/ 103/ 104/ 105/) csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ recons] : set bvecfile = /autofs/space/dbvecs.txt dali_001/ dali_002/ dali_003/ csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ recons] : set bvecfile =/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs/bvecs.txt csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ recons] : set bvalfile =/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r econs/bvals.txt csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ recons] : set doeddy = 1 csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ recons] : set dorotbvecs = 1 csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ recons] : set usemaskanat = 1 csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ recons] : set thrbet = 0.3 csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ recons] : set doregflt = 0 csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ recons] : set doregbbr = 1 csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ recons] : set doregmni = 1 csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ recons] : set doregcvs = 0
Re: [Freesurfer] Trac-all question
It can have any name you want. You just have to type the right name next to the -c ... On Fri, 2 Aug 2013, Alan Francis wrote: Sorry. I have another question. Should I name the config file dmrirc.txt or is there any other name? thank you so much, Alan On Fri, Aug 2, 2013 at 2:45 PM, Alan Francis alandarkene...@gmail.com wrote: Thanks Anastasia. On Fri, Aug 2, 2013 at 2:26 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Alan - All the set ... commands for tracula need to be in a configuration file. You then pass that configuration file as an argument to the -c option of trac-all. See tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Hope this helps, a.y On Fri, 2 Aug 2013, Alan Francis wrote: Hi Anastasia and others: I have been trying to run Trac all on five brains. It keeps giving me the error message: ERROR: run list is longer than subject list My run list is equal to the subject list: Here is the environment: Thanks for your help, Alan Martinos Center for Biomedical Imaging __ freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/stable5_3_0/ FSFAST_HOME /usr/local/freesurfer/stable5_3_0//fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/stable5_3_0//subjects MNI_DIR /usr/local/freesurfer/stable5_3_0//mni FSL_DIR /usr/pubsw/packages/fsl/current csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ Data/diffusion_ recons] : setenv SUBJECTS_DIR /autofs/space/d dali_001/ dali_002/ dali_003/ csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ Data/diffusion_ recons] : setenvSUBJECTS_DIR/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data /diffusion_r econs/ csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ Data/diffusion_ recons] : set dtroot = /autofs/space/d dali_001/ dali_002/ dali_003/ csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ Data/diffusion_ recons] : set dtroot=/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ r econs/ csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ Data/diffusion_ recons] : set subjlist = (101/ 102/ 103/ 104/ 105/) csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ Data/diffusion_ recons] : set dcmroot = /autofs/space/d dali_001/ dali_002/ dali_003/ csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ Data/diffusion_ recons] : set dcmroot=/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ r econs/ csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ Data/diffusion_ recons] : set dcmlist=(101/Diffusion_Recons/20080424_182054563000-12-01DTIValeras012a001 . nii \ ?102/Diffusion_Recons/20080911_101015358000-10-01DIFFUSIONHighResva l erabi1002s010a001.nii \ ?103/Diffusion_Recons/20080911_140753578000-10-01DIFFUSIONHighResva l eraBI1003s010a001.nii \ ?104/Diffusion_Recons/20080915_160812745000-10-01DIFFUSIONHighResVa l eraBI104s010a001.nii \ ?105/Diffusion_Recons/20080917_190940899000-16-01DIFFUSIONHighResVa l eraBI105s016a001.nii \ ? ) csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ Data/diffusion_ recons] : set runlist = (101/ 102/ 103/ 104/ bem/ mri/ stats/ touch/ Diffusion_Recons/ scripts/ surf/ trash/ label/ src/ tmp/ csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ Data/diffusion_ recons] : set runlist = (101/ 102/ 103/ 104/ 105/) csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ Data/diffusion_ recons] : set bvecfile = /autofs/space/dbvecs.txt dali_001/ dali_002/ dali_003/ csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ Data/diffusion_ recons] : set bvecfile=/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ r econs/bvecs.txt csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ Data/diffusion_ recons] : set bvalfile=/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ r econs/bvals.txt csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ Data/diffusion_ recons] : set doeddy = 1 csh::alanf@dali[/autofs/space/dali_003/users
Re: [Freesurfer] bvecs error from Tracula
Hi Amirhossein - The memory error doesn't occur when bbregister is running, but when dmri_train is running and loading the atlas data. You seem to have the snow leopard version of freesurfer installed, based on your build stamp (freesurfer-Darwin-snowleopard-__i686-stable-pub-v5.3.0). What version of the operating system do you have on your computer and how much memory? Thanks, a.y On Mon, 29 Jul 2013, amirhossein manzouri wrote: Hi, Kindly find attched the trac-all.log ! On Thu, Jul 25, 2013 at 6:25 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - If your error happens when bbregister is run, then it's not the error that the dmri_5.1_snow_leopard.tar.gz fix was meant to address. In any case that fix is not relevant to you b/c you're using 5.3 and not 5.1. Can you please send your trac-all.log to establish where exactly the error is happening? Thanks, a.y On Thu, 25 Jul 2013, amirhossein manzouri wrote: Hi ZeKe, I am getting this error during Tracula procedure somewhere between bbregister! BR On Jul 24, 2013 5:42 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Hello Amir, According to the log file you've attached, recon-all finished to completion without any errors. Are you sure you are encountering a memory error? If so, why? -Zeke On 07/24/2013 11:28 AM, amirhossein manzouri wrote: Kindly find attached the recon-all.log On Wed, Jul 24, 2013 at 4:50 PM, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu wrote: Hello Amir, Thanks for that... could you also please provide the recon-all.log file? It will be located in $SUBJECT_DIR/subject_name/__scripts/recon-all.log -Zeke On 07/24/2013 03:01 AM, amirhossein manzouri wrote: Hi, The content is : freesurfer-Darwin-snowleopard-__i686-stable-pub-v5.3.0 Can it help? On Mon, Jul 22, 2013 at 10:31 PM, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.__harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu wrote: Hello Amirhossein, Can you please provide me with the contents of build-stamp.txt in the /Applications/freesurfer directory? -Zeke On 07/22/2013 04:23 PM, amirhossein manzouri wrote: Hi, Yes I am getting the memory error with version 5.3, exactly the one that is reported in this link: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/0 1 9392.html https://mail.nmr.mgh.harvard.__edu/pipermail//freesurfer/__2011-July/0193 9 2.html https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/019392.h t ml Thanks, On Mon, Jul 22, 2013 at 8:15 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.__harvard.edu mailto:ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh. mailto:ayend...@nmr.mgh
Re: [Freesurfer] [tracula] error running trac-all -prep
Hi Florian - Do these files exist? /data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.mghdti.bvecs /data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.mghdti.bvals The format of the bvecs and bvals that you sent seems fine, but (and this has nothing to do with the error you're getting) I have to warn you that you may not be able to get good results running probabilistic tractography on this data. It looks like you're acquiring the same 6 diffusion directions, repeated 8 times. Six directions is the absolute minimum for reconstructing the tensor model, but will probably not be sufficient for the crossing fiber model that bedpostx reconstructs (and is used by tracula). Your scan time is better spent acquiring 48 different directions, rather than the same 6 directions 8 times. a.y On Mon, 29 Jul 2013, Borsodi Florian wrote: Hello, I have been trying to run tracula on my data and i keep getting the same kind of error repeatedly. For my imput I am using dicoms from a Siemens scanner with a stadard diffusion protocol. However, tracula cannot read the bvec and bval data out of the dicom header. Therefore, I implemented bvec and bval files into the config file. After doing so, I got the error which says that tracula cannot find the dwi_orig_flip.mghdti.bvecs and dwi_orig_flip.mghdti.bvals files. I have tried many options, but still cannot find a solution. I am hoping to get some troubleshooting help. I have atteched my log- and config- files, as well as my bvec and bval files. To uphold patient confidentiality, I have encode the name patient's data as AA. I believe the problems are the bvec and bval files or their structures. The log-file lete me assume this, especially the lines 202 - 205, 264 - 268 and 1480 - 1484. Thank you in advance for your help, and your speedy response. With kind regards, Florian Borsodi Department of Neurology Medical University of Graz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] correspondance between broadmann areas and freesurfer labels
There is a *.thresh.label version of all the BA labels in 5.3, but I don't think it's used by default. You can try using those labels instead. On Fri, 26 Jul 2013, Satrajit Ghosh wrote: hi bruce, currently 5.3, but the data i was looking at was processed with 5.1 and in that right ba44/45 was always larger. cheers, satra On Fri, Jul 26, 2013 at 9:47 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Satra, what version are you using? I think Anastasia implemented a thresholded version in 5.3, but perhaps she can comment. Bruce On Fri, 26 Jul 2013, Satrajit Ghosh wrote: hi bruce, related to this question, how are the stats/volumes of the BAs computed? cheers, satra On Fri, Jul 26, 2013 at 9:33 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Laouchedi that is a big research question! The answer is a qualified yes, but it depends strongly on what labels you mean. In general we find that the closer you are to primary areas like V1/M1, the stronger the correspondence is. We do supply some explicit estimates of Brodmann areas, have you looked at them? Bruce On Fri, 26 Jul 2013, LAOUCHEDI MAKHLOUF wrote: Hi i used freesurfer labels in a study and i want to identify the broadmann areas corresponding to some labels, is there any correspondence between the two ? Thanks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] correspondance between broadmann areas and freesurfer labels
You can search recon-all.log for the command that generates those stats and appply it to the ?h.BA.thresh.annot instead of ?h.BA.annot. On Fri, 26 Jul 2013, Satrajit Ghosh wrote: thanks guys. any thoughts on when the ba*.stats files will use these? right now i agree with bruce that they are biased by the predictability of the region. less accurate prediction - greater volume. cheers, satra On Fri, Jul 26, 2013 at 10:28 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: There is a *.thresh.label version of all the BA labels in 5.3, but I don't think it's used by default. You can try using those labels instead. On Fri, 26 Jul 2013, Satrajit Ghosh wrote: hi bruce, currently 5.3, but the data i was looking at was processed with 5.1 and in that right ba44/45 was always larger. cheers, satra On Fri, Jul 26, 2013 at 9:47 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Satra, what version are you using? I think Anastasia implemented a thresholded version in 5.3, but perhaps she can comment. Bruce On Fri, 26 Jul 2013, Satrajit Ghosh wrote: hi bruce, related to this question, how are the stats/volumes of the BAs computed? cheers, satra On Fri, Jul 26, 2013 at 9:33 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Laouchedi that is a big research question! The answer is a qualified yes, but it depends strongly on what labels you mean. In general we find that the closer you are to primary areas like V1/M1, the stronger the correspondence is. We do supply some explicit estimates of Brodmann areas, have you looked at them? Bruce On Fri, 26 Jul 2013, LAOUCHEDI MAKHLOUF wrote: Hi i used freesurfer labels in a study and i want to identify the broadmann areas corresponding to some labels, is there any correspondence between the two ? Thanks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] bvecs error from Tracula
Hi Amirhossein - If your error happens when bbregister is run, then it's not the error that the dmri_5.1_snow_leopard.tar.gz fix was meant to address. In any case that fix is not relevant to you b/c you're using 5.3 and not 5.1. Can you please send your trac-all.log to establish where exactly the error is happening? Thanks, a.y On Thu, 25 Jul 2013, amirhossein manzouri wrote: Hi ZeKe, I am getting this error during Tracula procedure somewhere between bbregister! BR On Jul 24, 2013 5:42 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Hello Amir, According to the log file you've attached, recon-all finished to completion without any errors. Are you sure you are encountering a memory error? If so, why? -Zeke On 07/24/2013 11:28 AM, amirhossein manzouri wrote: Kindly find attached the recon-all.log On Wed, Jul 24, 2013 at 4:50 PM, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu wrote: Hello Amir, Thanks for that... could you also please provide the recon-all.log file? It will be located in $SUBJECT_DIR/subject_name/__scripts/recon-all.log -Zeke On 07/24/2013 03:01 AM, amirhossein manzouri wrote: Hi, The content is : freesurfer-Darwin-snowleopard-__i686-stable-pub-v5.3.0 Can it help? On Mon, Jul 22, 2013 at 10:31 PM, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.__harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu wrote: Hello Amirhossein, Can you please provide me with the contents of build-stamp.txt in the /Applications/freesurfer directory? -Zeke On 07/22/2013 04:23 PM, amirhossein manzouri wrote: Hi, Yes I am getting the memory error with version 5.3, exactly the one that is reported in this link: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/01 9392.html https://mail.nmr.mgh.harvard.__edu/pipermail//freesurfer/__2011-July/01939 2.html https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/019392.ht ml Thanks, On Mon, Jul 22, 2013 at 8:15 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.__harvard.edu mailto:ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh. mailto:ayend...@nmr.mgh.__har__vard.edu http://harvard.edu mailto:ayend...@nmr.mgh.__harvard.edu mailto:ayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - That fix applied only to the 5.1 version. I'd recommend using the 5.3 version for tracula. Are you getting a memory error, and if so with which version? Thanks, a.y On Mon, 22 Jul 2013, amirhossein manzouri wrote: Dear Anastasia, I am trying to download the dmri_5.1_snow_leopard.tar.__gz from FreeSurfer website to solve memory problem but it is not available. Would you please check the source to the link? On Wed, Jul 17, 2013 at 5:51 PM, amirhossein manzouri a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com__ mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com
Re: [Freesurfer] bvecs error from Tracula
Hi Amirhossein - That fix applied only to the 5.1 version. I'd recommend using the 5.3 version for tracula. Are you getting a memory error, and if so with which version? Thanks, a.y On Mon, 22 Jul 2013, amirhossein manzouri wrote: Dear Anastasia, I am trying to download the dmri_5.1_snow_leopard.tar.gz from FreeSurfer website to solve memory problem but it is not available. Would you please check the source to the link? On Wed, Jul 17, 2013 at 5:51 PM, amirhossein manzouri a.h.manzo...@gmail.com wrote: The format of my bval file was wrong so I edited your file and tried and it worked, also bvec should be in three columns as you have mentioned before. On Wed, Jul 17, 2013 at 5:11 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Good to hear! Can you please share with all of us what was wrong with your original files? It may help others who have the same problem in the future. Thanks! On Wed, 17 Jul 2013, amirhossein manzouri wrote: Thanks Anastasia, IT HELPED! On Tue, Jul 16, 2013 at 5:25 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - I'm attaching sample files. a.y On Tue, 16 Jul 2013, amirhossein manzouri wrote: Hi Anastasia, I have tried both , 3-row and 3-column format and still wrong bvecc and bval from flip4fsl. Could you please send me a sample of your original files so I can compare? On Mon, Jul 15, 2013 at 7:44 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - Are your original bvecs/bvals in 3-row format instead of 3-column format? http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Thanks, a.y On Mon, 15 Jul 2013, amirhossein manzouri wrote: Dear Experts, I am running trac-all -prep -c dmrirc on my DWI data. After flip4fsl step I get the attached bval and bvec file which the bvec one is wrong so the process exits with error in dtifit. I have also attached original bvec and bval. -- Best regards, Amirhossein Manzouri The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] possible to use multiple B value DTI in Tracula?
Hi Sal - Are these different scans that you want to merge? If they're all in one file, then you just define the b-value for each frame as usual in the bvalfile. There's no rule that all the b-values have to be the same. Hope this helps, a.y On Sun, 21 Jul 2013, Salil Soman wrote: Hi, I was wondering - is it possible to use DTI data of multiple B values in Tracula (acquired during the same session and same TE)? Best wishes, Sal Salil Soman, MD, MS ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] [Tracula] Run trac-all with 2 time points for DTI scan but 1 time point for T1 scan. How to?
Hi Riccardo - The way this is designed is that you have to have longitudinal T1 data and run the longitudinal stream of recon-all on it, before you run the longitudinal version of tracula on your DWI. You could fake this by simply creating a copy of the recon-all directory of your first T1 time point and name it as the 2nd time point, then run longitudinal recon-all on them to generate all the files that tracula expects to find. This of course may bias your study towards the first time point, and the whole point of the longitudinal stream is to make sure there is no bias. Hope this helps, a.y On Mon, 22 Jul 2013, r.nava...@itab.unich.it wrote: Hi, I need to run trac-all on subjects scanned first time in T1 and DTI, second time DTI only. How to configure dmrirc? I've seen long.example but it seems that it require T1 second run too. Tnx, Riccardo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] bvecs error from Tracula
Good to hear! Can you please share with all of us what was wrong with your original files? It may help others who have the same problem in the future. Thanks! On Wed, 17 Jul 2013, amirhossein manzouri wrote: Thanks Anastasia, IT HELPED! On Tue, Jul 16, 2013 at 5:25 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - I'm attaching sample files. a.y On Tue, 16 Jul 2013, amirhossein manzouri wrote: Hi Anastasia, I have tried both , 3-row and 3-column format and still wrong bvecc and bval from flip4fsl. Could you please send me a sample of your original files so I can compare? On Mon, Jul 15, 2013 at 7:44 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - Are your original bvecs/bvals in 3-row format instead of 3-column format? http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Thanks, a.y On Mon, 15 Jul 2013, amirhossein manzouri wrote: Dear Experts, I am running trac-all -prep -c dmrirc on my DWI data. After flip4fsl step I get the attached bval and bvec file which the bvec one is wrong so the process exits with error in dtifit. I have also attached original bvec and bval. -- Best regards, Amirhossein Manzouri The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] bvecs error from Tracula
Hi Amirhossein - I'm attaching sample files. a.y On Tue, 16 Jul 2013, amirhossein manzouri wrote: Hi Anastasia, I have tried both , 3-row and 3-column format and still wrong bvecc and bval from flip4fsl. Could you please send me a sample of your original files so I can compare? On Mon, Jul 15, 2013 at 7:44 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - Are your original bvecs/bvals in 3-row format instead of 3-column format? http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Thanks, a.y On Mon, 15 Jul 2013, amirhossein manzouri wrote: Dear Experts, I am running trac-all -prep -c dmrirc on my DWI data. After flip4fsl step I get the attached bval and bvec file which the bvec one is wrong so the process exits with error in dtifit. I have also attached original bvec and bval. -- Best regards, Amirhossein Manzouri The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Best regards, Amirhossein Manzouri 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.586792 -0.376583 -0.716841 0.894195 0.022917 0.447091 0.729281 -0.410970 0.547041 -0.154251 0.964369 -0.214941 0.117136 0.773539 -0.622830 -0.407575 -0.414994 -0.813427 0.211330 0.753738 0.622269 0.095375 -0.969517 0.225700 -0.135450 -0.033490 -0.990218 -0.142125 -0.750521 -0.645383 -0.637009 0.746109 -0.193757 0.080563 0.971669 0.222192 0.106871 -0.021213 0.994047 0.298747 0.387214 0.872247 -0.207492 -0.803432 0.558072 0.331125 -0.040337 -0.942724 -0.805294 -0.589494 -0.063231 0.337278 -0.749774 -0.569282 0.592396 -0.761390 0.263348 -0.088979 -0.465650 0.880485 -0.527982 -0.430927 0.731803 -0.369111 -0.927082 0.065397 0.311914 0.926381 -0.211018 -0.684511 0.439336 -0.581746 -0.030114 -0.966623 -0.254425 -0.337568 0.744654 -0.575794 -0.574804 0.024806 -0.817915 0.271135 -0.747834 0.605996 -0.935185 0.185421 0.301743 0.889083 0.309665 -0.337104 -0.884343 0.033574 -0.465629 0.545045 0.586317 -0.599298 -0.350774 -0.016274 0.936319 0.416158 -0.900528 -0.125943 -0.732654 0.003250 0.680593 -0.739209 0.611423 0.282368 -0.256353 0.406875 -0.876776 -0.919023 0.372522 -0.128933 -0.257293 0.765486 0.589773 -0.589833 0.433953 0.681016 0.891136 -0.185957 -0.413881 0.679067 0.142105 -0.720190 -0.879811 -0.309554 0.360705 -0.621609 -0.697195 0.357102 0.897050 -0.430209 0.101102 -0.163347 0.417893 0.893691 -0.507183 -0.778309 -0.370136 0.107015 -0.446398 -0.888412 0.883485 0.435264 0.173205 0.598171 0.029843 0.800812 0.696192 0.698104 -0.167236 -0.393556 0.900808 0.183464 -0.761088 -0.402897 -0.508350 0.210324 0.396164 -0.893766 0.376032 -0.378955 0.845572 0.735763 -0.611461 -0.291148 -0.987214 -0.145866 -0.064273 0.529212 0.807365 0.260953 0.662918 0.472672 0.580621 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tracula -path option 0 unknown
Hi Gerit - Can you please send the entire trac-all.log for this subject? There could be some clues in the info that's printed out from the earlier steps, even if there's no outright error in those steps. Thanks, a.y On Fri, 5 Jul 2013, Gerit Pfuhl wrote: Dear Freesurfer experts, for one subject (out of over 80 already processed) I get i nthe last step an error I am unable to locate. The output from the tracula -path command says at the end: option 0 unknown. There are no reported problems in -prep, and -bedp. The script uses default values (I run this subject 3 times, always gets stuck on -path, not before). The subject was processed fine in tracule 5.1.0 with flt. Now in 5.2.0 we use bbr Excerpt of the output ... /igis/MRI_fs_rec_dti/64-10-094-1/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_5_std.txt /fastfs/igis/MRI_fs_rec_dti/64-10-094-1/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_4_std.txt /fastfs/igis/MRI_fs_rec_dti/64-10-094-1/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_4_std.txt /fastfs/igis/MRI_fs_rec_dti/64-10-094-1/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /fastfs/igis/MRI_fs_rec_dti/64-10-094-1/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /fastfs/igis/MRI_fs_rec_dti/64-10-094-1/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt /fastfs/igis/MRI_fs_rec_dti/64-10-094-1/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt ERROR: Option 0 unknown Thanks for all help to understand this Gerit ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] application of mri_cvs_register question
Hi Matt - For how to tell tracula to use CVS registration, see Specify the inter-subject registration method here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Does this answer your question? a.y On Mon, 8 Jul 2013, Hoptman, Matthew wrote: Hi all, I see how to apply mri_vol2vol to DTI data from dt_recon, but I’m not clear on how to do so to DTI data processed in Tracula. The command in the “Multimodal integration and inter-subject registration” tutorial is: mri_vol2vol --targ templateid --m3z morph.m3z --noDefM3zPath --reg 2anat.register.dat --mov diffvol --o diffvol2CVS --no-save-reg But in Tracula, there are no “register.dat” files, or indeed no *.dat files. Is there a way to convert one of the *.mat files in the dmri/xfms directory to a *.dat file? Also, given that I think Tracula and dt_recon use different transformation algorithms, which Tracula transform should I choose? Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _ Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - My guess is that it's something about the file dmri/dwi_orig.mghdti.bvals that's causing the error. Could you please send along that file? Also, how did you fix your previous configuration file problem? Letting the list know about the resolution of the issue would help other users, who may have the same issue in the future and search the list archives. It'll also help me figure out if there are any checks I could add to trac-all to preclude this. Thanks! a.y On Tue, 9 Jul 2013, Gundran, Andrew wrote: Helo all, I was finally able to figure out my configuration file problem. But when I run the first step of pre-processing I receive an error about freesurfer being unable to read a certain dwi_frame file. ln -sf /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi.nii.gz /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/data.nii.gz awk: can't open file 1000 source line number 1 mri_concat --i /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz --mean --o /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/lowb.nii.gz niiRead(): error opening file /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 I have also attached the trac-all log. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Editing the endpoint ROIs, and re-running trac-all -path
Hi Susie - The initial placement of the control points plays a much bigger role than the end ROIs. The path being initialized in a bad location would be more of a problem than the end ROIs being too generous. So I'd check rh.unc_AS_avg32_mni_bbr_cpts_5.nii.gz before editing the end ROIs. Does that look like it's better placed on right than the left? I'd also check if the brain mask (aparc+aseg_mask) is any different in that area on one side. Hope this helps, a.y On Tue, 9 Jul 2013, Susan Kuo wrote: Hi Anastasia, For one of my subjects, I am noticing that the right uncinate fasciculus is very diffuse and more importantly, erroneously crosses from the frontal to the temporal lobe. I looked at the original endpoint ROI generated by trac-all -prior (rh.unc_AS_avg33_mni_bbr_end1.nii.gz) and the dilated endpoint ROI in the temporal lobe (rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz) and noticed that the endpoints appeared to cross over into the frontal lobe. Attached is a snapshot for your perusal. On the left side is a display of the subject/dmri/dtifit_FA.nii with the subject/dpath/rh.unc_AS_avg33_mni_bbr/path.pd.nii.gz tract superimposed over. As you can see, the right unc tract crosses from the frontal to the temporal lobe. On the right side is a display of the subject/dmri/brain_anat_mni.nii.gz with the endpoints subject/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end2.nii.gz in green and subject/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end1.nii.gz in blue (the red dots are control points). As you can see, the blue endpoints bleed over from the temporal to the frontal lobe. I tried to eliminate these blue points with fslview and then writing over rh.unc_AS_avg33_mni_bbr_end1.nii.gz. I performed a similar function manually editing rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz to better reflect the boundaries . I subsequently tried to re-run trac-all -path, and unfortunately, all my tracts looked much worse. Do you know if incorrectly placed endpoints impair the path reconstruction? Do you think you can help me? Any advice you can give would be much appreciated. -- Susie Kuo NIH Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] bvecs error from Tracula
Hi Amirhossein - Are your original bvecs/bvals in 3-row format instead of 3-column format? http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Thanks, a.y On Mon, 15 Jul 2013, amirhossein manzouri wrote: Dear Experts, I am running trac-all -prep -c dmrirc on my DWI data. After flip4fsl step I get the attached bval and bvec file which the bvec one is wrong so the process exits with error in dtifit. I have also attached original bvec and bval. -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] application of mri_cvs_register question
Hi Matt - The CVS morph under xfms/cvs/ maps the individual anatomical to the CVS template. To map from individual diffusion to the CVS template, you'd have to first use diffusion-to-anatomical affine transform file under xfms/. Hope this helps, a.y On Mon, 15 Jul 2013, Hoptman, Matthew wrote: Hi Anastasia, Not really, what I now have is: subject/dmri/xfms/cvs Within cvs, there are anatomical files that are registered to the CVS template, as below, but what I DON'T have is the application of these transforms to the DTI data. That's what I'm trying to puzzle out. The files in subject/dmri/xfms/cvs are: c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051306.log c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051310.log final_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz final_CVSmorph_tocvs_avg35_inMNI152.m3z lh.dbg_surf.pial lh.dbg_surf.white lh.resample.aparc.annot lh.resample.pial lh.resample.white nlalign-afteraseg-norm.mgz nlalign-aseg.mgz rh.dbg_surf.pial rh.dbg_surf.white rh.resample.aparc.annot rh.resample.pial rh.resample.white summary.c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051306.log summary.c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051310.log transform.txt -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 12:19 PM To: Hoptman, Matthew Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] application of mri_cvs_register question Hi Matt - For how to tell tracula to use CVS registration, see Specify the inter-subject registration method here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Does this answer your question? a.y On Mon, 8 Jul 2013, Hoptman, Matthew wrote: Hi all, I see how to apply mri_vol2vol to DTI data from dt_recon, but I’m not clear on how to do so to DTI data processed in Tracula. The command in the “Multimodal integration and inter-subject registration” tutorial is: mri_vol2vol --targ templateid --m3z morph.m3z --noDefM3zPath --reg 2anat.register.dat --mov diffvol --o diffvol2CVS --no-save-reg But in Tracula, there are no “register.dat” files, or indeed no *.dat files. Is there a way to convert one of the *.mat files in the dmri/xfms directory to a *.dat file? Also, given that I think Tracula and dt_recon use different transformation algorithms, which Tracula transform should I choose? Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _ Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise
Re: [Freesurfer] pathstats.byvoxel.txt
That is exactly right! Those were added after 5.1. On Mon, 15 Jul 2013, Susan Kuo wrote: Hi Anastasia, I believe the issue I had with the pathstats.byvoxel.txt not displaying the last four values (AD_Avg RD_Avg MD_Avg FA_Avg ) is owing to the fact that trac-all was run with FREESURFER 5.1. I believe that FREESURFER 5.2 may be needed to generate path.pd.trk, and from that, the above values are derived. Is this correct? Thank you again, and have a good day! -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] pathstats.byvoxel.txt
I should add that there several other reasons to be using the newer version of tracula (from 5.2 or 5.3), including speed and other improvements listed here: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates Also note that using 5.2 or 5.3 won't make a difference in terms of the tracula code, but for recon-all purposes you should not be using 5.2. On Mon, 15 Jul 2013, Susan Kuo wrote: Hi Anastasia, I believe the issue I had with the pathstats.byvoxel.txt not displaying the last four values (AD_Avg RD_Avg MD_Avg FA_Avg ) is owing to the fact that trac-all was run with FREESURFER 5.1. I believe that FREESURFER 5.2 may be needed to generate path.pd.trk, and from that, the above values are derived. Is this correct? Thank you again, and have a good day! -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] application of mri_cvs_register question
Hi Matt - The --reg option expects a .dat file. There should be one produced by bbregister in the xfms/ directory? a.y On Mon, 15 Jul 2013, Hoptman, Matthew wrote: Hi Anastasia, Yes, that was my problem. I think I need to use mri_vol2vol --targ ../../../cvs_avg35_inMNI152/mri/norm.mgz --m3z ../../cvs/cvs_avg35_inMNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z --noDefM3zPath --reg diff2anat.bbr.mat --mov ../dtifit_FA.nii.gz --o diffvol2CVS.nii.gz --no-save-reg I now get: Using the m3z file as it is; no assumed location. regio_read_register(): Success Error reading R[3][0] from diff2anat.bbr.mat Matrix from regfile: -0.001 0.972 -0.234 -3.311; -0.001 0.234 0.972 69.949; 0.000 0.000 0.000 1.000; 0.000 0.000 0.000 0.000; I was stuck at that point. Lilla Zollei told me she'd look into it, but maybe you've communicated with her? Thanks Matt -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 2:30 PM To: Hoptman, Matthew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] application of mri_cvs_register question Hi Matt - The CVS morph under xfms/cvs/ maps the individual anatomical to the CVS template. To map from individual diffusion to the CVS template, you'd have to first use diffusion-to-anatomical affine transform file under xfms/. Hope this helps, a.y On Mon, 15 Jul 2013, Hoptman, Matthew wrote: Hi Anastasia, Not really, what I now have is: subject/dmri/xfms/cvs Within cvs, there are anatomical files that are registered to the CVS template, as below, but what I DON'T have is the application of these transforms to the DTI data. That's what I'm trying to puzzle out. The files in subject/dmri/xfms/cvs are: c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051306.log c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051310.log final_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz final_CVSmorph_tocvs_avg35_inMNI152.m3z lh.dbg_surf.pial lh.dbg_surf.white lh.resample.aparc.annot lh.resample.pial lh.resample.white nlalign-afteraseg-norm.mgz nlalign-aseg.mgz rh.dbg_surf.pial rh.dbg_surf.white rh.resample.aparc.annot rh.resample.pial rh.resample.white summary.c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051306.log summary.c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051310.log transform.txt -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 12:19 PM To: Hoptman, Matthew Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] application of mri_cvs_register question Hi Matt - For how to tell tracula to use CVS registration, see Specify the inter-subject registration method here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Does this answer your question? a.y On Mon, 8 Jul 2013, Hoptman, Matthew wrote: Hi all, I see how to apply mri_vol2vol to DTI data from dt_recon, but I’m not clear on how to do so to DTI data processed in Tracula. The command in the “Multimodal integration and inter-subject registration” tutorial is: mri_vol2vol --targ templateid --m3z morph.m3z --noDefM3zPath --reg 2anat.register.dat --mov diffvol --o diffvol2CVS --no-save-reg But in Tracula, there are no “register.dat” files, or indeed no *.dat files. Is there a way to convert one of the *.mat files in the dmri/xfms directory to a *.dat file? Also, given that I think Tracula and dt_recon use different transformation algorithms, which Tracula transform should I choose? Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _ Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you
Re: [Freesurfer] application of mri_cvs_register question
Got it. Can you send me a listing of the contents of the xfms/ directory? Conversions b/w formats can be done with tkregister2, but the .dat file should normally be there since it's the default format for bbregister. On Mon, 15 Jul 2013, Hoptman, Matthew wrote: Right, that's been my problem :( Maybe something went wrong, but I didn't see any problem in the log files. Actually, the command I showed below had a typo (I used --mat rather than --reg to get that error). Is there a way to convert *.mat to *.dat? -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 2:44 PM To: Hoptman, Matthew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] application of mri_cvs_register question Hi Matt - The --reg option expects a .dat file. There should be one produced by bbregister in the xfms/ directory? a.y On Mon, 15 Jul 2013, Hoptman, Matthew wrote: Hi Anastasia, Yes, that was my problem. I think I need to use mri_vol2vol --targ ../../../cvs_avg35_inMNI152/mri/norm.mgz --m3z ../../cvs/cvs_avg35_inMNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z --noDefM3zPath --reg diff2anat.bbr.mat --mov ../dtifit_FA.nii.gz --o diffvol2CVS.nii.gz --no-save-reg I now get: Using the m3z file as it is; no assumed location. regio_read_register(): Success Error reading R[3][0] from diff2anat.bbr.mat Matrix from regfile: -0.001 0.972 -0.234 -3.311; -0.001 0.234 0.972 69.949; 0.000 0.000 0.000 1.000; 0.000 0.000 0.000 0.000; I was stuck at that point. Lilla Zollei told me she'd look into it, but maybe you've communicated with her? Thanks Matt -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 2:30 PM To: Hoptman, Matthew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] application of mri_cvs_register question Hi Matt - The CVS morph under xfms/cvs/ maps the individual anatomical to the CVS template. To map from individual diffusion to the CVS template, you'd have to first use diffusion-to-anatomical affine transform file under xfms/. Hope this helps, a.y On Mon, 15 Jul 2013, Hoptman, Matthew wrote: Hi Anastasia, Not really, what I now have is: subject/dmri/xfms/cvs Within cvs, there are anatomical files that are registered to the CVS template, as below, but what I DON'T have is the application of these transforms to the DTI data. That's what I'm trying to puzzle out. The files in subject/dmri/xfms/cvs are: c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051306.log c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051310.log final_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz final_CVSmorph_tocvs_avg35_inMNI152.m3z lh.dbg_surf.pial lh.dbg_surf.white lh.resample.aparc.annot lh.resample.pial lh.resample.white nlalign-afteraseg-norm.mgz nlalign-aseg.mgz rh.dbg_surf.pial rh.dbg_surf.white rh.resample.aparc.annot rh.resample.pial rh.resample.white summary.c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051306.log summary.c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051310.log transform.txt -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 12:19 PM To: Hoptman, Matthew Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] application of mri_cvs_register question Hi Matt - For how to tell tracula to use CVS registration, see Specify the inter-subject registration method here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Does this answer your question? a.y On Mon, 8 Jul 2013, Hoptman, Matthew wrote: Hi all, I see how to apply mri_vol2vol to DTI data from dt_recon, but I’m not clear on how to do so to DTI data processed in Tracula. The command in the “Multimodal integration and inter-subject registration” tutorial is: mri_vol2vol --targ templateid --m3z morph.m3z --noDefM3zPath --reg 2anat.register.dat --mov diffvol --o diffvol2CVS --no-save-reg But in Tracula, there are no “register.dat” files, or indeed no *.dat files. Is there a way to convert one of the *.mat files in the dmri/xfms directory to a *.dat file? Also, given that I think Tracula and dt_recon use different transformation algorithms, which Tracula transform should I choose? Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE
Re: [Freesurfer] application of mri_cvs_register question
Hi Matt - Try anatorig2diff.bbr.dat. a.y On Mon, 15 Jul 2013, Hoptman, Matthew wrote: Hi Anastasia, Here it is: anat2anatorig.dat anatorig2diff.bbr.dat anatorig2diff.bbr.dat.sum diff2mni.bbr.mat anat2anatorig.dat~ anatorig2diff.bbr.dat~ anatorig2diff.bbr.mat mni2anat.mat anat2anatorig.mat anatorig2diff.bbr.dat.log anatorig2mni.mat mni2anatorig.mat anat2diff.bbr.mat anatorig2diff.bbr.dat.log.old cvs mni2diff.bbr.mat anat2mni.matanatorig2diff.bbr.dat.mincost diff2anat.bbr.mat anatorig2anat.mat anatorig2diff.bbr.dat.paramdiff2anatorig.bbr.mat -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 2:56 PM To: Hoptman, Matthew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] application of mri_cvs_register question Got it. Can you send me a listing of the contents of the xfms/ directory? Conversions b/w formats can be done with tkregister2, but the .dat file should normally be there since it's the default format for bbregister. On Mon, 15 Jul 2013, Hoptman, Matthew wrote: Right, that's been my problem :( Maybe something went wrong, but I didn't see any problem in the log files. Actually, the command I showed below had a typo (I used --mat rather than --reg to get that error). Is there a way to convert *.mat to *.dat? -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 2:44 PM To: Hoptman, Matthew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] application of mri_cvs_register question Hi Matt - The --reg option expects a .dat file. There should be one produced by bbregister in the xfms/ directory? a.y On Mon, 15 Jul 2013, Hoptman, Matthew wrote: Hi Anastasia, Yes, that was my problem. I think I need to use mri_vol2vol --targ ../../../cvs_avg35_inMNI152/mri/norm.mgz --m3z ../../cvs/cvs_avg35_inMNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z --noDefM3zPath --reg diff2anat.bbr.mat --mov ../dtifit_FA.nii.gz --o diffvol2CVS.nii.gz --no-save-reg I now get: Using the m3z file as it is; no assumed location. regio_read_register(): Success Error reading R[3][0] from diff2anat.bbr.mat Matrix from regfile: -0.001 0.972 -0.234 -3.311; -0.001 0.234 0.972 69.949; 0.000 0.000 0.000 1.000; 0.000 0.000 0.000 0.000; I was stuck at that point. Lilla Zollei told me she'd look into it, but maybe you've communicated with her? Thanks Matt -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 2:30 PM To: Hoptman, Matthew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] application of mri_cvs_register question Hi Matt - The CVS morph under xfms/cvs/ maps the individual anatomical to the CVS template. To map from individual diffusion to the CVS template, you'd have to first use diffusion-to-anatomical affine transform file under xfms/. Hope this helps, a.y On Mon, 15 Jul 2013, Hoptman, Matthew wrote: Hi Anastasia, Not really, what I now have is: subject/dmri/xfms/cvs Within cvs, there are anatomical files that are registered to the CVS template, as below, but what I DON'T have is the application of these transforms to the DTI data. That's what I'm trying to puzzle out. The files in subject/dmri/xfms/cvs are: c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051306.log c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051310.log final_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz final_CVSmorph_tocvs_avg35_inMNI152.m3z lh.dbg_surf.pial lh.dbg_surf.white lh.resample.aparc.annot lh.resample.pial lh.resample.white nlalign-afteraseg-norm.mgz nlalign-aseg.mgz rh.dbg_surf.pial rh.dbg_surf.white rh.resample.aparc.annot rh.resample.pial rh.resample.white summary.c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051306.log summary.c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051310.log transform.txt -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 12:19 PM To: Hoptman, Matthew Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] application of mri_cvs_register question Hi Matt - For how to tell tracula to use CVS registration, see Specify the inter-subject registration method here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Does this answer your question? a.y On Mon, 8 Jul 2013, Hoptman, Matthew wrote: Hi all, I see how to apply mri_vol2vol to DTI data from dt_recon, but I’m not clear on how to do so to DTI data processed in Tracula. The command in the “Multimodal integration and inter-subject registration” tutorial is: mri_vol2vol --targ templateid --m3z morph.m3z --noDefM3zPath --reg 2anat.register.dat --mov diffvol --o diffvol2CVS --no-save-reg But in Tracula, there are no “register.dat” files
Re: [Freesurfer] [tracula] running into trouble with nifti data
Hi Satra - There are 2 ways to put things in proper orientation for fsl tools: 1. L-R flip the gradient vectors: This is a hack, in the sense that it anticipates that FSL will treat your volume as L-R flipped when it has a certain type of orientation, but now you've broken your bvecs for the purposes of any software that doesn't do that (like freesurfer). 2. Convert both the volume and the gradient vectors to LAS orientation: This is not a hack, in the sense that now you have volumes and vectors that work both for FSL and otherwise, and work regardless of the original orientation. Obviously, you want to do 1 OR 2, not both. What's breaking things for you is that your preprocessing is doing 1 and then trac-all preprocessing does 2. I've opted for 2 in trac-all b/c I need the files to work for both FSL i/o routines (in bedpostx, most critically) and for freesurfer i/o routines (in my own code for tracula). Alternatively, I could keep two sets of everything and feed one set into the FSL routines and the other into the freesurfer routines, but this would be inelegant, a pain to implement, a recipe for introducing bugs, and, unltimately, a sure way to wipe out whatever little is left of my sanity. Any other aspect of default preprocessing in trac-all (eddy currents, susceptibility) can be turned off if you want to use another method to do it. But it's not possible to turn off this way of making things compatible with FSL to use that way of making things compatible with FSL. If you want to try it, you can replace every instance of flip4fsl with cp and let me know what happens, I'd be really curious. Hope this helps, a.y On Tue, 2 Jul 2013, Satrajit Ghosh wrote: hi ay, so this is what i did. i flipped the gradient LR intentionally, ran flip4fsl and then dtifit and now the eigenvec 1 looks good, but not if i run dtifit prior to flip4fsl. but this brings me back to my original point which is that my image and the gradients are (i think) already in proper orientation for fsl tools (since the preflip output in the previous email looks correct) and flip4fsl is making it inappropriate for fsl. also as some additional info: - yes this is the siemens 60 dir scan but that predefined gradient table doesn't take into account the slice orientation - if you use dcm2nii to extract these dicoms, the first two gradients are: 0.996362388134 0.0389195755124 -0.07581084221601 -0.65292024612426 0.00993375014513 -0.75736147165298 this is because dcm2nii, much like DTIPrep takes the image orientation matrix into account when doing the conversion, which mri_convert doesn't. so i think tracula should have an option of not flipping 4 fsl in the scenario where other processes (e.g., my script, dcm2nii) automatically take care of generating an fsl compatible file + gradient info. please let me know if i'm misinterpreting something here. cheers, satra On Tue, Jul 2, 2013 at 8:21 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Satra - What you're showing in the screenshots would be consistent with a L-R flip of the gradient directions, which is what my comparison of your gradients to the original Siemens gradients indicated. (Assuming the data was acquired with the standard Siemens 60 gradient directions.) a.y On Tue, 2 Jul 2013, Satrajit Ghosh wrote: hi ay, i'll look into the orientations a little later tonight, but here is V1 overlaid on FA for preflip and postflip execution of dtifit. cheers, satra On Tue, Jul 2, 2013 at 7:48 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Satra - The orientation of your dwi_orig.nii.gz is LPS. What flip4fsl will do is convert it to LAS, and perform the same conversion on the gradient table that you provide. This of course assumes that dwi_orig.nii.gz and your gradient table are consistent as they come out of your custom preprocessing. Is there any chance that they're not? Looking at the sample data set that you sent me, I can only see what came out of your preprocessing and not what went in. I'm assuming that this is from the standard Siemens 60 direction sequence, and it has 57 directions b/c 3 of them were thrown out by your preprocessing. I don't know which directions were thrown out obviously, but the first 2 directions in your gradient table are: -0.99699027939850948 -0.057720153020443053 0.051758263409041924 0.63287878858184599 0.066164234845749903
Re: [Freesurfer] [tracula] running into trouble with nifti data
Hi Satra - The orientation of your dwi_orig.nii.gz is LPS. What flip4fsl will do is convert it to LAS, and perform the same conversion on the gradient table that you provide. This of course assumes that dwi_orig.nii.gz and your gradient table are consistent as they come out of your custom preprocessing. Is there any chance that they're not? Looking at the sample data set that you sent me, I can only see what came out of your preprocessing and not what went in. I'm assuming that this is from the standard Siemens 60 direction sequence, and it has 57 directions b/c 3 of them were thrown out by your preprocessing. I don't know which directions were thrown out obviously, but the first 2 directions in your gradient table are: -0.99699027939850948 -0.057720153020443053 0.051758263409041924 0.63287878858184599 0.066164234845749903 0.77141869630019422 The first two directions in the Siemens 60 direction gradient table are: 1.00 0.00 0.00 0.5867917880 -0.3765825401 -0.7168409782 There's not only a small adjustment of the direction but also a sign change there. So I'd look into that. Let me know if any of my assumptions about your original data is wrong. a.y On Tue, 2 Jul 2013, Satrajit Ghosh wrote: hi anastasia, i'm trying to debug a seg fault that some folks are seeing deep into a tracula run. process: 1. feed dicoms to a script that runs DTIPrep and outputs a nifti file, bvec, bval (among checking for many artifacts, this reduces the b=0 volumes to a single registered mean volume, runs eddy correction, discards bad directions, reorients the gradients appropriately and generates a report of the quality) 2. run tracula on this nifti file observation: when i run fsl/dtifit on the same nifti file + bvec + bval, i get the proper orientation for eigvec1 lines. however, when i feed this into tracula, the output of the dtifit step looks terrible - i.e. the lines are not oriented as how one might expect water to diffuse. suspicion: although i have not reached the crash yet, i believe it might be related to this fact that the gradients are not oriented properly relative to the volume. i also suspect that this has something to do with the flip4fsl step inside tracula, which is possibly unnecessary because fsl already likes the input files. but it seems this step is encoded quite heavily within the trac-all scripts. questions: a. is there a quick way to turn the flip4fsl step off? b. alternatively do you have any suggestions for what to do here? the whole point of running through DTIPrep is to clean up the data before giving it to tracula or other programs, so i would really like to keep that step. cheers, satra ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] [tracula] running into trouble with nifti data
Hi Satra - What you're showing in the screenshots would be consistent with a L-R flip of the gradient directions, which is what my comparison of your gradients to the original Siemens gradients indicated. (Assuming the data was acquired with the standard Siemens 60 gradient directions.) a.y On Tue, 2 Jul 2013, Satrajit Ghosh wrote: hi ay, i'll look into the orientations a little later tonight, but here is V1 overlaid on FA for preflip and postflip execution of dtifit. cheers, satra On Tue, Jul 2, 2013 at 7:48 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Satra - The orientation of your dwi_orig.nii.gz is LPS. What flip4fsl will do is convert it to LAS, and perform the same conversion on the gradient table that you provide. This of course assumes that dwi_orig.nii.gz and your gradient table are consistent as they come out of your custom preprocessing. Is there any chance that they're not? Looking at the sample data set that you sent me, I can only see what came out of your preprocessing and not what went in. I'm assuming that this is from the standard Siemens 60 direction sequence, and it has 57 directions b/c 3 of them were thrown out by your preprocessing. I don't know which directions were thrown out obviously, but the first 2 directions in your gradient table are: -0.99699027939850948 -0.057720153020443053 0.051758263409041924 0.63287878858184599 0.066164234845749903 0.77141869630019422 The first two directions in the Siemens 60 direction gradient table are: 1.00 0.00 0.00 0.5867917880 -0.3765825401 -0.7168409782 There's not only a small adjustment of the direction but also a sign change there. So I'd look into that. Let me know if any of my assumptions about your original data is wrong. a.y On Tue, 2 Jul 2013, Satrajit Ghosh wrote: hi anastasia, i'm trying to debug a seg fault that some folks are seeing deep into a tracula run. process: 1. feed dicoms to a script that runs DTIPrep and outputs a nifti file, bvec, bval (among checking for many artifacts, this reduces the b=0 volumes to a single registered mean volume, runs eddy correction, discards bad directions, reorients the gradients appropriately and generates a report of the quality) 2. run tracula on this nifti file observation: when i run fsl/dtifit on the same nifti file + bvec + bval, i get the proper orientation for eigvec1 lines. however, when i feed this into tracula, the output of the dtifit step looks terrible - i.e. the lines are not oriented as how one might expect water to diffuse. suspicion: although i have not reached the crash yet, i believe it might be related to this fact that the gradients are not oriented properly relative to the volume. i also suspect that this has something to do with the flip4fsl step inside tracula, which is possibly unnecessary because fsl already likes the input files. but it seems this step is encoded quite heavily within the trac-all scripts. questions: a. is there a quick way to turn the flip4fsl step off? b. alternatively do you have any suggestions for what to do here? the whole point of running through DTIPrep is to clean up the data before giving it to tracula or other programs, so i would really like to keep that step. cheers, satra The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly
Re: [Freesurfer] Tracula/ config file error
Hi Andrew - I'm sorry that you're annoyed. I can feel your pain. Take a deep breath and let it all go. More to the point, when I view the text file that you sent, I see that several of the lines are joined together, so both the dcmroot and dcmlist variables appear commented out. Is this intentional? Was this text file saved on a unix system? a.y On Mon, 1 Jul 2013, Gundran, Andrew wrote: I have been trying to run tracula with a config file but keep getting the same error message when I use the trac-all command for pre-processing set: Variable name must begin with a letter It has become very, very annoying. PLEASE SOMEONE HELP!!! Andrew -- # FreeSurfer SUBJECTS_DIR # /home/baileype/Desktop/JG005/freesurfer/mri # setenv SUBJECTS_DIR /home/baileype/Desktop/JG005 # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /home/baileype/Desktop/JG005 # Subject IDs # set subjlist = (freesurfer) # In case you want to analyze only Huey and Louie # Default: Run analysis on all subjects # set runlist = (1) # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile and bvalfile must be specified (see below) # set dcmroot = /home/baileype/Desktop/JG005 set dcmlist = (DKI.nii.gz) # Diffusion gradient table # Must be specified if inputs are not MGH DICOMs # Three-column format, one row for each volume in the diffusion data set # Default: Read from DICOM header # set bvecfile = /home/baileype/Desktop/JG005/bvecs # Diffusion b-value table # Must be specified if inputs are not MGH DICOMs # Single-column format, one value for each volume in the diffusion data set # Default: Read from DICOM header # set bvalfile = /home/baileype/Desktop/JG005/bvals # Perform registration-based B0-inhomogeneity compensation? # Default: 0 (no) # # set dob0 = 1 # Input B0 field map magnitude DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0mlist = (huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm louie/fmag/XXX-1.dcm) # Input B0 field map phase DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0plist = (huey/fphas/XXX-1.dcm dewey/fphas/XXX-1.dcm louie/fphas/XXX-1 # Echo spacing for field mapping sequence (from sequence printout) # Only used if dob0 = 1 # Default: None # # set echospacing = 0.7 # Perform registration-based eddy-current compensation? # Default: 1 (yes) # set doeddy = 1 # Rotate diffusion gradient vectors to match eddy-current compensation? # Only used if doeddy = 1 # Default: 1 (yes) # set dorotbvecs = 1 # Fractional intensity threshold for BET mask extraction from low-b images # This mask is used only if usemaskanat = 0 # Default: 0.3 # set thrbet = 0.2 # Perform diffusion-to-T1 registration by flirt? # Default: 0 (no) # set doregflt = 0 # Perform diffusion-to-T1 registration by bbregister? # Default: 1 (yes) # set doregbbr = 1 # Perform registration of T1 to MNI template? # Default: 1 (yes) # set doregmni = 1 # MNI template # Only used if doregmni = 1 # Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # # set mnitemp = /path/to/mni_template.nii.gz # Perform registration of T1 to CVS template? # Default: 0 (no) # # set doregcvs = 0 # CVS template subject ID # Only used if doregcvs = 1 # Default: cvs_avg35 # # set cvstemp = donald # Parent directory of the CVS template subject # Only used if doregcvs = 1 # Default: $FREESURFER_HOME/subjects # # set cvstempdir = /path/to/cvs/atlases/of/ducks # Use brain mask extracted from T1 image instead of low-b diffusion image? # Has no effect if there is no T1 data # Default: 1 (yes) # set usemaskanat = 1 # Paths to reconstruct # Default: All paths in the atlas # set pathlist = (lh.cst_AS rh.cst_AS \ lh.unc_AS rh.unc_AS \ lh.ilf_AS rh.ilf_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.ccg_PP rh.ccg_PP \ lh.cab_PP rh.cab_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP) # Number of path control points # It can be a single number for all paths or a different number for each of the # paths specified in pathlist # Default: 7 for the forceps major, 6 for the corticospinal tract, # 4 for the angular bundle, and 5 for all other paths # set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5) # List of training subjects # This text file lists the locations of training subject directories # Default: $FREESURFER_HOME/trctrain/trainlist.txt # set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt # Number of sticks (anisotropic diffusion compartments) in the bedpostx # ball-and-stick model # Default: 2 # set nstick = 2 # Number of MCMC burn-in iterations # (Path
Re: [Freesurfer] Tracula/ config file error
Can you see that this is all one line? # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile and bvalfile must be specified (see below) # set dcmroot = /home/baileype/Desktop/JG005 set dcmlist = (DKI.nii.gz) On Mon, 1 Jul 2013, Gundran, Andrew wrote: Yes, the text was saved on a unix system -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Monday, July 01, 2013 2:34 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula/ config file error Hi Andrew - I'm sorry that you're annoyed. I can feel your pain. Take a deep breath and let it all go. More to the point, when I view the text file that you sent, I see that several of the lines are joined together, so both the dcmroot and dcmlist variables appear commented out. Is this intentional? Was this text file saved on a unix system? a.y On Mon, 1 Jul 2013, Gundran, Andrew wrote: I have been trying to run tracula with a config file but keep getting the same error message when I use the trac-all command for pre-processing set: Variable name must begin with a letter It has become very, very annoying. PLEASE SOMEONE HELP!!! Andrew -- # FreeSurfer SUBJECTS_DIR # /home/baileype/Desktop/JG005/freesurfer/mri # setenv SUBJECTS_DIR /home/baileype/Desktop/JG005 # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /home/baileype/Desktop/JG005 # Subject IDs # set subjlist = (freesurfer) # In case you want to analyze only Huey and Louie # Default: Run analysis on all subjects # set runlist = (1) # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile and bvalfile must be specified (see below) # set dcmroot = /home/baileype/Desktop/JG005 set dcmlist = (DKI.nii.gz) # Diffusion gradient table # Must be specified if inputs are not MGH DICOMs # Three-column format, one row for each volume in the diffusion data set # Default: Read from DICOM header # set bvecfile = /home/baileype/Desktop/JG005/bvecs # Diffusion b-value table # Must be specified if inputs are not MGH DICOMs # Single-column format, one value for each volume in the diffusion data set # Default: Read from DICOM header # set bvalfile = /home/baileype/Desktop/JG005/bvals # Perform registration-based B0-inhomogeneity compensation? # Default: 0 (no) # # set dob0 = 1 # Input B0 field map magnitude DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0mlist = (huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm louie/fmag/XXX-1.dcm) # Input B0 field map phase DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0plist = (huey/fphas/XXX-1.dcm dewey/fphas/XXX-1.dcm louie/fphas/XXX-1 # Echo spacing for field mapping sequence (from sequence printout) # Only used if dob0 = 1 # Default: None # # set echospacing = 0.7 # Perform registration-based eddy-current compensation? # Default: 1 (yes) # set doeddy = 1 # Rotate diffusion gradient vectors to match eddy-current compensation? # Only used if doeddy = 1 # Default: 1 (yes) # set dorotbvecs = 1 # Fractional intensity threshold for BET mask extraction from low-b images # This mask is used only if usemaskanat = 0 # Default: 0.3 # set thrbet = 0.2 # Perform diffusion-to-T1 registration by flirt? # Default: 0 (no) # set doregflt = 0 # Perform diffusion-to-T1 registration by bbregister? # Default: 1 (yes) # set doregbbr = 1 # Perform registration of T1 to MNI template? # Default: 1 (yes) # set doregmni = 1 # MNI template # Only used if doregmni = 1 # Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # # set mnitemp = /path/to/mni_template.nii.gz # Perform registration of T1 to CVS template? # Default: 0 (no) # # set doregcvs = 0 # CVS template subject ID # Only used if doregcvs = 1 # Default: cvs_avg35 # # set cvstemp = donald # Parent directory of the CVS template subject # Only used if doregcvs = 1 # Default: $FREESURFER_HOME/subjects # # set cvstempdir = /path/to/cvs/atlases/of/ducks # Use brain mask extracted from T1 image instead of low-b diffusion image? # Has no effect if there is no T1 data # Default: 1 (yes) # set usemaskanat = 1 # Paths to reconstruct # Default: All paths in the atlas # set pathlist = (lh.cst_AS rh.cst_AS \ lh.unc_AS rh.unc_AS \ lh.ilf_AS rh.ilf_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.ccg_PP rh.ccg_PP \ lh.cab_PP rh.cab_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP) # Number of path control points # It can be a single number for all paths or a different
Re: [Freesurfer] Tracula/ config file error
What program are you viewing it in? If you add a line at the end of config.txt that says echo $dcmlist (without the quotation marks) and then run source config.txt on the command line, does it print out DKI.nii.gz? On Mon, 1 Jul 2013, Gundran, Andrew wrote: It reads like # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile and bvalfile must be specified (see below) # set dcmroot = /home/baileype/Desktop/JG005 set dcmlist = (DKI.nii.gz) -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Monday, July 01, 2013 2:48 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula/ config file error Can you see that this is all one line? # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile and bvalfile must be specified (see below) # set dcmroot = /home/baileype/Desktop/JG005 set dcmlist = (DKI.nii.gz) On Mon, 1 Jul 2013, Gundran, Andrew wrote: Yes, the text was saved on a unix system -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Monday, July 01, 2013 2:34 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula/ config file error Hi Andrew - I'm sorry that you're annoyed. I can feel your pain. Take a deep breath and let it all go. More to the point, when I view the text file that you sent, I see that several of the lines are joined together, so both the dcmroot and dcmlist variables appear commented out. Is this intentional? Was this text file saved on a unix system? a.y On Mon, 1 Jul 2013, Gundran, Andrew wrote: I have been trying to run tracula with a config file but keep getting the same error message when I use the trac-all command for pre-processing set: Variable name must begin with a letter It has become very, very annoying. PLEASE SOMEONE HELP!!! Andrew -- # FreeSurfer SUBJECTS_DIR # /home/baileype/Desktop/JG005/freesurfer/mri # setenv SUBJECTS_DIR /home/baileype/Desktop/JG005 # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /home/baileype/Desktop/JG005 # Subject IDs # set subjlist = (freesurfer) # In case you want to analyze only Huey and Louie # Default: Run analysis on all subjects # set runlist = (1) # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile and bvalfile must be specified (see below) # set dcmroot = /home/baileype/Desktop/JG005 set dcmlist = (DKI.nii.gz) # Diffusion gradient table # Must be specified if inputs are not MGH DICOMs # Three-column format, one row for each volume in the diffusion data set # Default: Read from DICOM header # set bvecfile = /home/baileype/Desktop/JG005/bvecs # Diffusion b-value table # Must be specified if inputs are not MGH DICOMs # Single-column format, one value for each volume in the diffusion data set # Default: Read from DICOM header # set bvalfile = /home/baileype/Desktop/JG005/bvals # Perform registration-based B0-inhomogeneity compensation? # Default: 0 (no) # # set dob0 = 1 # Input B0 field map magnitude DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0mlist = (huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm louie/fmag/XXX-1.dcm) # Input B0 field map phase DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0plist = (huey/fphas/XXX-1.dcm dewey/fphas/XXX-1.dcm louie/fphas/XXX-1 # Echo spacing for field mapping sequence (from sequence printout) # Only used if dob0 = 1 # Default: None # # set echospacing = 0.7 # Perform registration-based eddy-current compensation? # Default: 1 (yes) # set doeddy = 1 # Rotate diffusion gradient vectors to match eddy-current compensation? # Only used if doeddy = 1 # Default: 1 (yes) # set dorotbvecs = 1 # Fractional intensity threshold for BET mask extraction from low-b images # This mask is used only if usemaskanat = 0 # Default: 0.3 # set thrbet = 0.2 # Perform diffusion-to-T1 registration by flirt? # Default: 0 (no) # set doregflt = 0 # Perform diffusion-to-T1 registration by bbregister? # Default: 1 (yes) # set doregbbr = 1 # Perform registration of T1 to MNI template? # Default: 1 (yes) # set doregmni = 1 # MNI template # Only used if doregmni = 1 # Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # # set mnitemp = /path/to/mni_template.nii.gz # Perform registration of T1 to CVS template? # Default: 0 (no) # # set doregcvs = 0 # CVS template subject ID # Only used if doregcvs = 1 # Default: cvs_avg35 # # set cvstemp = donald # Parent directory of the CVS template subject # Only used
Re: [Freesurfer] Tracula/ config file error
That probably means you're not running a C shell. That's fine, can you instead try running trac-all and see if it prints out the value of dcmlist now that you've added that line? I'll repeat my other question: What program are you using to view the text file? On Mon, 1 Jul 2013, Gundran, Andrew wrote: Whoops. It doesn't read like that every # is a new line along with each set I did that and the error was Line13: syntax error near unexpected token `(' Line 13: `set subjlist = (freesurfer) -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Monday, July 01, 2013 3:09 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula/ config file error What program are you viewing it in? If you add a line at the end of config.txt that says echo $dcmlist (without the quotation marks) and then run source config.txt on the command line, does it print out DKI.nii.gz? On Mon, 1 Jul 2013, Gundran, Andrew wrote: It reads like # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile and bvalfile must be specified (see below) # set dcmroot = /home/baileype/Desktop/JG005 set dcmlist = (DKI.nii.gz) -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Monday, July 01, 2013 2:48 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula/ config file error Can you see that this is all one line? # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile and bvalfile must be specified (see below) # set dcmroot = /home/baileype/Desktop/JG005 set dcmlist = (DKI.nii.gz) On Mon, 1 Jul 2013, Gundran, Andrew wrote: Yes, the text was saved on a unix system -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Monday, July 01, 2013 2:34 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula/ config file error Hi Andrew - I'm sorry that you're annoyed. I can feel your pain. Take a deep breath and let it all go. More to the point, when I view the text file that you sent, I see that several of the lines are joined together, so both the dcmroot and dcmlist variables appear commented out. Is this intentional? Was this text file saved on a unix system? a.y On Mon, 1 Jul 2013, Gundran, Andrew wrote: I have been trying to run tracula with a config file but keep getting the same error message when I use the trac-all command for pre-processing set: Variable name must begin with a letter It has become very, very annoying. PLEASE SOMEONE HELP!!! Andrew -- # FreeSurfer SUBJECTS_DIR # /home/baileype/Desktop/JG005/freesurfer/mri # setenv SUBJECTS_DIR /home/baileype/Desktop/JG005 # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /home/baileype/Desktop/JG005 # Subject IDs # set subjlist = (freesurfer) # In case you want to analyze only Huey and Louie # Default: Run analysis on all subjects # set runlist = (1) # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile and bvalfile must be specified (see below) # set dcmroot = /home/baileype/Desktop/JG005 set dcmlist = (DKI.nii.gz) # Diffusion gradient table # Must be specified if inputs are not MGH DICOMs # Three-column format, one row for each volume in the diffusion data set # Default: Read from DICOM header # set bvecfile = /home/baileype/Desktop/JG005/bvecs # Diffusion b-value table # Must be specified if inputs are not MGH DICOMs # Single-column format, one value for each volume in the diffusion data set # Default: Read from DICOM header # set bvalfile = /home/baileype/Desktop/JG005/bvals # Perform registration-based B0-inhomogeneity compensation? # Default: 0 (no) # # set dob0 = 1 # Input B0 field map magnitude DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0mlist = (huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm louie/fmag/XXX-1.dcm) # Input B0 field map phase DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0plist = (huey/fphas/XXX-1.dcm dewey/fphas/XXX-1.dcm louie/fphas/XXX-1 # Echo spacing for field mapping sequence (from sequence printout) # Only used if dob0 = 1 # Default: None # # set echospacing = 0.7 # Perform registration-based eddy-current compensation? # Default: 1 (yes) # set doeddy = 1 # Rotate diffusion gradient vectors to match eddy-current compensation? # Only used if doeddy = 1 # Default: 1 (yes) # set dorotbvecs = 1 # Fractional intensity threshold for BET mask extraction from low-b images # This mask is used only if usemaskanat = 0
Re: [Freesurfer] [FreeSurfer] Corpus Callosum tracts
Hi Roxana - How tracula works is decribed in detail here: http://www.frontiersin.org/Journal/DownloadFile.ashx?pdf=1FileId=8155articleId=10815Version=1ContentTypeId=21FileName=fninf-05-00023.pdf To add a new tract to the tracula atlas that is not currently part of it, the tract would first have to be labeled manually in the 33 subjects that make up our atlas. Hope this helps, a.y On Wed, 26 Jun 2013, Teodorescu, Roxana wrote: Dear FreeSurfers, I would like to get the tracts in Corpus Callosum body, not just the forceps major and forceps minor given by tracula. Is there a way to get that with Tracula? Thank you. Roxana. --- Roxana O. Teodorescu, PhD Postdoctoral Fellow Department of Neurology Mount Sinai School of Medicine ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Fwd: DTI questions
Sorry, can't open the image. On Sun, 23 Jun 2013, Rotem Saar wrote: Hi there, Long time:). Well I wrote to the list several times regarding high FA values I got when performing DTI analysis. Today we know that the problem was an additional direction (we had 17 directions instead of 16 - we used a Philips scanner,1.5T). So we deleted the additional slices and the high values indeed disappeared, but then another problem came up (tried several subjects so the problem is not specific to a subject) - I noticed an artifact that I can't explain - please see the attached pictures. This artifact existed even before I deleted the additional slices, also - I see the artifact also when loading the masked volume...It is cyclic - run over all slices... any ideas ? I'm using version 5.2 and I know the command lines are correct (send it to u in the past). Thanks for your help Rotem ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Fwd: DTI questions
Hi Rotem - No problem. Were these scans by any chance acquired with a coronal slice prescription? In the axial views that you sent, the artifact that you're pointing to looks like misalignment between consecutive coronal slices, which could be due to head motion. a.y On Tue, 25 Jun 2013, Rotem Saar wrote: Dear Anastasia, I tried several times to upload these images in a non-compressed way, but they were too big and my posts were rejected, with no opportunity for any other upload way. Is there any other way for me to upload it so that everyone can see it ? Attached are the images in a non-compressed fashion. I will be very happy if u will have a look, and post your answer to me and the list to save some time, until I will be able to consider another way to upload them. I know that we should write to all the list, but at the moment if the images are not visible this won't help - so I will really appreciate if u will have a look but also tell me what is the best way to upload them so that all list members will be able to see them. Thank u very much for your help. Rotem 2013/6/25 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Sorry, can't open the image. On Sun, 23 Jun 2013, Rotem Saar wrote: Hi there, Long time:). Well I wrote to the list several times regarding high FA values I got when performing DTI analysis. Today we know that the problem was an additional direction (we had 17 directions instead of 16 - we used a Philips scanner,1.5T). So we deleted the additional slices and the high values indeed disappeared, but then another problem came up (tried several subjects so the problem is not specific to a subject) - I noticed an artifact that I can't explain - please see the attached pictures. This artifact existed even before I deleted the additional slices, also - I see the artifact also when loading the masked volume...It is cyclic - run over all slices... any ideas ? I'm using version 5.2 and I know the command lines are correct (send it to u in the past). Thanks for your help Rotem The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Possible to generate connectivity map using FS and Tracula
Hi Sal - Not sure what you mean by connectivity maps, can you be more specific? Tracula is not a method for exploratory analyses of the type what is my seed region connected to? It's a method for reconstructing a set of 18 major white-matter pathways, which are listed here: http://www.frontiersin.org/Journal/DownloadFile.ashx?pdf=1FileId=8155articleId=10815Version=1ContentTypeId=21FileName=fninf-05-00023.pdf Hope this helps, a.y On Thu, 20 Jun 2013, Salil Soman wrote: Dear Doug, Is there a way to use the Freesurfer and Tracula output to compute connectivity maps? Thanks! Sal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] TRACULA - tract volume and length
Hi Fred - As with any probabilistic method, volume here is a measure of the spread of the probability distribution of the pathway (i.e. of path.pd.nii.gz), so it can be interpreted as the amount of uncertainty in the data. A more spread out distribution means more uncertainty, a tighter distribution means less uncertainty. Please note that TRACULA performs tractography in each subject's native DWI space, so volume/length are not calculated in a common/normalized space for all subjects. So beware when comparing volume/length across subjects. If you use the weighted FA/MD/etc measures, these are weighted by the value of the probability distribution at every voxel, so they are the mean values in a probabilistic sense. Hope this helps, a.y On Wed, 19 Jun 2013, Fred Sanders wrote: Dear DTI experts, I am trying to understand how to interpret tract length volume measurements that TRACULA provides. For example, let’s say a clinical population differs from a control group in mean FA of a particular tract, and tract length volume are comparable across the 2 groups. I think this would support the notion that the tract’s diffusion properties are indeed different across the two groups and that the FA finding are unlikely to be an artifact of probabilistic tractography. Is this a correct interpretation? Conversely, if group differences in tract volumes were detected, would you recommend comparing mean FA across the two group while covarying for tract volume? Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] generate pathstats.overall.txt file from tract volume
Sorry, there's no command that will generate that file for anything other than the output generated by tracula, but if you want to average FA etc over a volume it's pretty easy to do with fslstats. On Fri, 14 Jun 2013, Jayachandra Raghava wrote: Hello All, Is it possible to generate pathstats.overall.txt file from tract volume? I would like to do some tract statistics on the tract volumes generated by FSL. Best Jay ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Coupling cortical and TRACULA results
You can find the aparc+aseg mapped from T1 space to DWI space in the dlabel/diff directory. You can overlay it on the paths reconstructed from tracula to see which aparc+aseg labels the paths overlap with. The identities of the labels in the aparc+aseg are in $FREESURFER_HOME/FreeSurferColorLUT.txt. On Mon, 10 Jun 2013, std...@virgilio.it wrote: Hi list, Thiebaut de Schotten et al., in an article on cortex (Monkey to human comparative anatomy of the frontal lobe association tracts reported that The superior longitudinal fasciculus has three distinct branches (Petrides and Pandya, 1984). In humans, the first branch of the superior longitudinal fasciculus (SLF I) connects to the superior parietal lobule and precuneus (BA 5 and 7), to the superior frontal (BA 8, 9, 32) and perhaps to some anterior cingulate areas (BA 24). The second branch (SLF II) originatesin the anterior intraparietal sulcus and the angular gyrus (BA 39 and 40) and terminates in the posterior regions of the superior and middle frontal gyrus (BA 6, 8, 9). The third branch (SLF III) connects the intraparietal sulcus and inferior parietal lobule to the inferior frontal gyrus (BA 44, 45, 47) By TRACULA output we have 2 output SLFp and SLFt. Having also cortical results, I wonder if possible to know which are the seed and target areas of SLF p and SLFt or al least to know which is that branch that is described by SLFp output. Thanks, Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] averaging tracts?
Hi Matt - Thanks for your kind words! The merged_*.mgz file is just a 4D mgz file where each frame corresponds to one of the 18 tracts. The only special thing about this mgz file is that it has some special fields in its header that tell freeview how to display each tract (color, name, and threshold). I haven't tried this, but I would guess that if you performed any operation on that mgz file, those header fields would be preserved. And if they're not they should be, so we should know about it. You can try to map each mgz file from individual DWI space to a common space with mri_vol2vol and then average them with mri_concat. Let us know if this ends up working or if you have any questions about these steps. Thanks! a.y On Thu, 6 Jun 2013, Hoptman, Matthew wrote: Hi all, Thanks for tracula , which I think is a terrific tool. Is there any way to average tracts across subjects for viewing purposes? I have in mind somehting along the line of a group average merged_avg33_mni_bbi.mgz. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] R: R: Re: R: Re: Tracula
This issue has come up on the list a few times recently. Please search for your error in the email archives before posting to the list. Thanks. On Thu, 6 Jun 2013, std...@virgilio.it wrote: Hi Anastasia, I have resolved the previous problem by writing configuration file with sudo nano in command line. Now I'm running trac-all -prep but I have this error: writing registered surface to/Applications/freesurfer/subjects/subject_prova/Diff03/surf/rh.cvs.tocvs_av g35.sphere.reg... expanding nbhd size to 1 mris_resample: Command not found. What's happened? Thanks, Stefano Messaggio originale Da: std...@virgilio.it Data: 6-giu-2013 0.51 A: ayend...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Ogg: [Freesurfer] R: Re: R: Re: Tracula I obtain /Applications/freesurfer/subjects/subject_prova my DWI file is in Diff01, Diff02 ... that are in subject_prova folder. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 6-giu-2013 0.42 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: Tracula What do you get when you run echo $SUBJECTS_DIR? On Thu, 6 Jun 2013, std...@virgilio.it wrote: Hi Anastasia, yes, I have check the SUBJECTS_DIR. I do not understand why all previous configuration file start normally and this no. Do you note some line that might be wrong additionally to setenv SUBJECTS_DIR line. Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 5-giu-2013 16.09 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: Tracula Is the setenv SUBJECTS_DIR line really commented out? You must set SUBJECTS_DIR, see the example configuration file on the wiki and under $FREESURFER_HOME/bin/dmrirc.example. On Wed, 5 Jun 2013, std...@virgilio.it wrote: Hi list and Anastasia, I'm performing a set of data with tracula version 3.0. I have change my dmrirc file respect to previous analyses and now I have one problem set: Variable name must begin with a letter. ERROR: must specify as many DWI dicoms as subjects. I do not find the line that is wrong. I think to have approximately used the same lines of previous and correct analysis. I have attached the configuration file. Note that I'm using nii.gz. Thanks and best regards. Stefano The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula
Is the setenv SUBJECTS_DIR line really commented out? You must set SUBJECTS_DIR, see the example configuration file on the wiki and under $FREESURFER_HOME/bin/dmrirc.example. On Wed, 5 Jun 2013, std...@virgilio.it wrote: Hi list and Anastasia, I'm performing a set of data with tracula version 3.0. I have change my dmrirc file respect to previous analyses and now I have one problem set: Variable name must begin with a letter. ERROR: must specify as many DWI dicoms as subjects. I do not find the line that is wrong. I think to have approximately used the same lines of previous and correct analysis. I have attached the configuration file. Note that I'm using nii.gz. Thanks and best regards. Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] R: Re: Tracula
What do you get when you run echo $SUBJECTS_DIR? On Thu, 6 Jun 2013, std...@virgilio.it wrote: Hi Anastasia, yes, I have check the SUBJECTS_DIR. I do not understand why all previous configuration file start normally and this no. Do you note some line that might be wrong additionally to setenv SUBJECTS_DIR line. Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 5-giu-2013 16.09 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: Tracula Is the setenv SUBJECTS_DIR line really commented out? You must set SUBJECTS_DIR, see the example configuration file on the wiki and under $FREESURFER_HOME/bin/dmrirc.example. On Wed, 5 Jun 2013, std...@virgilio.it wrote: Hi list and Anastasia, I'm performing a set of data with tracula version 3.0. I have change my dmrirc file respect to previous analyses and now I have one problem set: Variable name must begin with a letter. ERROR: must specify as many DWI dicoms as subjects. I do not find the line that is wrong. I think to have approximately used the same lines of previous and correct analysis. I have attached the configuration file. Note that I'm using nii.gz. Thanks and best regards. Stefano The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tracula error
Hi Skyler - When you say it's been working fine, have you checked that the orientations are correct by viewing dtifit_V1.nii.gz and dtifit_FA.nii.gz, like in the snapshot that I sent you? If those orientations aren't correct, the gradient table isn't correct either. a.y On Tue, 21 May 2013, Skyler Gabriel Shollenbarger wrote: Hi Anastasia, Thank you for all of your help! 'trac-all' has been working fine with the other subjects, so it doesn't appear to be the gradient vector file. Yes, unfortunately the resolution is not the best. Would you consider this subject a loss or are there other fixes you suggest? Thanks again! Skyler - Original Message - From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: sholl...@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, May 21, 2013 10:40:59 AM Subject: Re: [Freesurfer] tracula error Hi Skyler - A couple of things. I'm attaching a screenshot of the FA map and primary tensor eigenvectors of your subject. First, it looks like your gradient directions are incorrect, given how the eigenvectors are oriented in the corpus callosum (yellow arrows in the coronal and axial slice). The eigenvectors follow the shape of the corpus callosum in the axial view but not in the coronal view. My guess is your gradient vectors need to be flipped in the z-direction. Second, your resolution is 4mm. There's going to be a lot of partial voluming. You'll have to give up on the thinner tracts, like ccg/cab (see purple arrow in sagittal view pointing to cingulum, you can barely resolve it from the corpus callosum). Third, you have 14 gradient directions, so fitting the ball-and-stick model to this data, which is done by bedpostx and which you need for the tract reconstruction step, is going to be challening. I don't want to discourage you, but tractography may be a bit more than this data can support. Please let me know if you have more questions, a.y On Mon, 20 May 2013, sholl...@uwm.edu wrote: Hi Anastasia, They were uploaded. Thanks for your help! Skyler Sent from my iPhone On May 20, 2013, at 10:20 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Skyler - If you upload the dmri/dmri.bedpostX/dlabel/scripts directories of your subject for me, I'll take a look. http://gate.nmr.mgh.harvard.edu/filedrop2/ a.y On Fri, 17 May 2013, sholl...@uwm.edu wrote: Hi Anastasia, The brain mask looks fine. Any other suggestions? Thanks for your help, Skyler Sent from my iPhone On May 17, 2013, at 12:24 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Skyler - How does the brain mask look like? Any major chunks of brain missing in the area of the left uncinate? That's the tract where the error occurs, and based on this info in the log file, I'm guessing it's a masking issue: [...] INFO: Rejected 4221 streamlines for straying off mask INFO: Rejected 2 streamlines for reversing direction INFO: Rejected 9 streamlines as length outliers INFO: Have 56 total streamlines (min/mean/max length: 1/13/33) [...] Hope this helps, a.y On Wed, 15 May 2013, Skyler Gabriel Shollenbarger wrote: Hi all, We ran tracula prep stage and it exited with errors: 'Selected streamline has fewer than 5 points'. We have attached the log and error files if needed. Thank you in advance! Skyler The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Tracula problem
Hi Matt - Yes, the dcmroot variable can be used if you have the same root directory for *all* input files. If not, don't define dcmroot and instead give the full path to each input file. Then you shouldn't have to modify any scrips. a.y On Fri, 17 May 2013, Hoptman, Matthew wrote: Hi Anastasia, I solved this particular problem in a new dmrirc, but it seemed that I had to modify trac-all to remove the ${dcmroot} in front of: infile, b0mfile and b0pfile: diff bin/trac-preproc bin/trac-preproc.orig if ($#dcmroot 0) set infile = $infile --- if ($#dcmroot 0) set infile = $dcmroot/$infile 259c259 endif --- endif 296c296 set dcmfile = $b0mfile --- set dcmfile = $dcmroot/$b0mfile 311c311 set dcmfile = $b0pfile --- set dcmfile = $dcmroot/$b0pfile But now it doesn't seem to loop through the subjects, so I'm doing them one at a time (painful). Also, if, as in my other question, I try to run this as a cluster job, I don't know how I can substitute a new subject into subjlist. I have 64 subjects and would like to do trac-all -prep -c dmri on all of them simultaneously. I have used bedpostx in SGE, but there you can just write loop to get it to go through your subjects. If I could make the subject variable external to dmrirc, I could do easily script the trac-all job to run in SGE, but I can't fiugre out how to pass it to the trac-all command. Is there any way to pass the subject number directly to the command? Does this make sense? Matt -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Friday, May 17, 2013 12:31 PM To: Hoptman, Matthew Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula problem Hi Matt - Can you source try this on the command line: source dmrirc_53beta echo $b0mlist echo $b0plist Are these filenames correct, do these files exist? This is how you define them in your configuration file: set b0mlist = (`ls ${subjlist}/fmag/MR.* | sort -n | head -1`) set b0plist = (`ls ${SUBJECTS_DIR}/${subjlist}/fphas/ | sort -n | head -1`) Thanks, a.y On Wed, 15 May 2013, Hoptman, Matthew wrote: Hi all, I’m having a problem with tracula. I’m trying to run in version 5.3 beta (is that version very different from the newer 5.3?). If I run trac-preproc -c dmrirc –prep, I get: mri_convert /home/hoptman/freesurfer/subjects/c159032/ /home/hoptman/freesurfer/subjects/c159032/dmri/b0mag.nii.gz mri_convert /home/hoptman/freesurfer/subjects/c159032/ /home/hoptman/freesurfer/subjects/c159032/dmri/b0mag.nii.gz corRead(): can't open file /home/hoptman/freesurfer/subjects/c159032/COR-.info I don’t know why it would look for COR-.info in the subjects’ root directory. I’m attaching my dmrirc file in case that helps. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. __ Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error
Re: [Freesurfer] DTI metrics along the whole tract?
Hi Celine - The way this average is computed for pathstats.byvoxel.txt is by averaging the values for each one of the sample paths that are drawn by the MCM algorithm. This essentially weighted sinced voxels that more sample paths go through will be counted more than voxels that fewer sample paths go through. a.y On Fri, 17 May 2013, cel...@nmr.mgh.harvard.edu wrote: Hi Anastasia I am very sorry I didn't see this email so it may be a doubloon with my question I just post. Indeed I am interested in a profile of the DTI metrics along the tract. So if I take the average value of each section it can give me a kind of profile, and so I was just wondering if taking a weighted metrics would be possible in order to remove values that are a bit far from the highest probability of the tract. Thanks a lot! Celine Hi Celine - Since 5.2, there are 2 types of measures in the pathstats.byvoxel.txt file: The value at every point along the trajectory sampled at roughly the center of the bundle, or the value at every point along the trajectory averaged over the width of the bundle. Sorry, there are no other measures available at this point. If I understand correctly, you would like to see something like a profile of the measure of interest at every point along the trajectory? a.y On Mon, 6 May 2013, cel...@nmr.mgh.harvard.edu wrote: Hi Tracula team I am using tracula to study the corticospinal tract in a patient population. I am wondering if there would be a way to have the different DTI metrics from the whole tract at different depth/portion of the tracts. Something like the information given by the pathstats.byvoxel.txt file, but for the whole width of the tract? If not, do you see a way to sample the value of the diffusion metrics on a certain tract starting from the cortex (like with projfrac or projdist with the WM surface)? Thanks very much for your help Celine ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula longitudinal nan values for highest probability path
Hi Vincent - Thanks for bringing this to my attention. I can see what might cause this glitch (only in the longitudinal case) and I'll fix it in the next version. In the meantime, if you delete one of the two identical lines from cpts.map.txt, and then rerun the dmri_pathstats command line that you'll find in the trac-all.log of your subject, it should regenerate the stats files correctly. Sorry for the inconvenience. a.y On Fri, 17 May 2013, vbrun...@nmr.mgh.harvard.edu wrote: Dear Anastasia, When running the longitudinal tracula version on our 39 subjects I found for some of them nan-values for the center_avg variables of some tracts. When I have a look at the tract distribution and the highest probability path, everything seems to be ok. However, when checking the control points of this path, two of them are the same. Do you know how this could have happened / what to do? E.g. control points of forceps major from a subject (cpts.map.txt), see 4th and 5th control point: 63 20 39 67 31 39 59 43 38 52 42 38 52 42 38 43 32 38 50 19 33 And the respective pathstats.overall.txt: Count 1500 Volume 370 Len_Min 62 Len_Max 99 Len_Avg 78.9307 Len_Center 0 AD_Avg 0.00155598 AD_Avg_Weight 0.00158424 AD_Avg_Center -nan RD_Avg 0.000438439 RD_Avg_Weight 0.000401328 RD_Avg_Center -nan MD_Avg 0.000810952 MD_Avg_Weight 0.000795633 MD_Avg_Center -nan FA_Avg 0.662419 FA_Avg_Weight 0.696257 FA_Avg_Center -nan Thanks for your help!! :) Best, Vincent ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula longitudinal nan values for highest probability path
Hi Vincent - If you upload the tracula dirs for this particular time point, I'll take a look. a.y On Mon, 20 May 2013, Vincent Brunsch wrote: Hi Anastasia, Thanks for your help! I had this issue with 4 tracts in total. I just want to add that before rerunning dmri_pathstats not only pathstats.overall but also pathstats.byvoxel was affected (in the latter there were no matrix entries at all). I found some information in the trac-all.log but not explicitly the command line - this was found in pathstats.overall.txt, though. After rerunning dmri_pathstats everything looks great now for 3 out of the 4 tracts, YEAH! I am not sure what to do with the last one, though: Here, the same error occurs but in cpts.map.txt no two lines are identical: For lh.cst: 58 48 10 62 51 21 65 55 26 70 58 35 72 57 39 64 55 56 Would you suggest deleting randomly one time point for this tract of this subject? Thanks! Vincent Am 5/20/2013 10:31 AM, schrieb Anastasia Yendiki: Hi Vincent - Thanks for bringing this to my attention. I can see what might cause this glitch (only in the longitudinal case) and I'll fix it in the next version. In the meantime, if you delete one of the two identical lines from cpts.map.txt, and then rerun the dmri_pathstats command line that you'll find in the trac-all.log of your subject, it should regenerate the stats files correctly. Sorry for the inconvenience. a.y On Fri, 17 May 2013, vbrun...@nmr.mgh.harvard.edu wrote: Dear Anastasia, When running the longitudinal tracula version on our 39 subjects I found for some of them nan-values for the center_avg variables of some tracts. When I have a look at the tract distribution and the highest probability path, everything seems to be ok. However, when checking the control points of this path, two of them are the same. Do you know how this could have happened / what to do? E.g. control points of forceps major from a subject (cpts.map.txt), see 4th and 5th control point: 63 20 39 67 31 39 59 43 38 52 42 38 52 42 38 43 32 38 50 19 33 And the respective pathstats.overall.txt: Count 1500 Volume 370 Len_Min 62 Len_Max 99 Len_Avg 78.9307 Len_Center 0 AD_Avg 0.00155598 AD_Avg_Weight 0.00158424 AD_Avg_Center -nan RD_Avg 0.000438439 RD_Avg_Weight 0.000401328 RD_Avg_Center -nan MD_Avg 0.000810952 MD_Avg_Weight 0.000795633 MD_Avg_Center -nan FA_Avg 0.662419 FA_Avg_Weight 0.696257 FA_Avg_Center -nan Thanks for your help!! :) Best, Vincent ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] TRACULA outputs out of expected range
Hi Ali - The last row of your gradient table is 0 0 0. And yet, based on the b-value table, it is supposed to correspond to a diffusion-weighted volume with b=800. So there must have been a diffusion-encoding gradient vector that was applied to acquire that volume, and you need to find out what that gradient vector was and put it in that line. Also, some of the lines in the gradient table follow the Xe-Y notation and some don't. I don't know if this will cause a problem, it's possible that it might depending on the platform. In any case, it's good to be consistent to be safe. Hope this helps, a.y On Mon, 6 May 2013, Ali Ezzati wrote: Hi Anastasia, I think I still have the previous problem of out of range outputs. For example: based on literature ( your previous TRACULA-bases articles) the expected range of mean FA value is around 0.4-0.5, but the average FA for my data is 0.7-0.8. The same is true with MD, RD, AD values. Comparative analysis between groups is not promising too. This makes me think something is going wrong with my analysis/settings, although I get no error during processing. I can only think of settings in .dmricr or bvec file to be a source of error, so I have attached a sample of them for one of the subjects to this email. I would be grateful if you could take a look at them and let me know if they are as expected. There are 3 .bvec files inside the dmri folder: 1- dwi_orig.mghdti.bvecs 2- bvecs.norot 3- bvecs The first 2 files are the same as my input .bvec file (bvecs.norot is rotated to 3 rows instead of 3 columns). File 3 -bevecs- is different from the other 2 files. Thank you again for your help, Ali From: Ali Ezzati Sent: Friday, May 03, 2013 11:54 AM To: Anastasia Yendiki Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] TRACULA outputs out of expected range Hi Anastasia, Thank you for your response. I think I figured out what was the problem: The delimiter for the 3 column .bvec file MUST be SPACE/TAB, otherwise the program fails to reshape it correctly. In my case the delimiter was , and the program was reading only the 1st column of it. I have one more question: I know that FA values might differ from study to study and from MRI to MRI, but what is a reasonable range for that after analysis with Tracula? In your study (20011) the range was ~ 0.3-0.6. But for in elderly population the average is around 0.2 higher. Does it sound normal to you? I was not able to find any study using your method in elderly population for comparison. Thank you, Ali From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Tuesday, April 30, 2013 3:11 PM To: Ali Ezzati Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA outputs out of expected range Hi Ali - This is unusual. It may have something to do with system settings. Can you send an example of the two versions of the bvecs files that have the different values? Thanks, a.y On Mon, 29 Apr 2013, Ali Ezzati wrote: Hello Experts, I would be grateful if you could help me with this problem: I was able to run all steps of TRACULA on several subjects without any error message, but all the final outcomes (FA,MD,RD,AD values) are out of the expected range (i.e average FA values for all tracts are 1). I tried to identify the source of this problem... clearly FA values in dmri/dtifit_FA, which is an output of prep step are all out of range. The only source of error that I can think of is .bvecs file. My input .bvecs files are in 3 columns, exactly as described in the manual. There are two .bvecs file in the dmri folder. one is dwi_orig.mghdti.bvecs which is exactly the same as my input .bvecs file and the other one's name is just bvecs, which has completely different values. Could this be the source of my problem? or something else is causing this. Thank you, Ali The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] incomplete forceps
Hi Benjamin - This means that the initial guess for the path based on the atlas average is way off, due to poor alignment between your subject and the atlas subejcts. Ways to get around this is to look into the options for registration, whether diffusion-to-anatomical or anatomical-to-atlas, and to increase the number of control points used for fminor. Hope this helps, a.y On Mon, 6 May 2013, Roschinski, Benjamin wrote: Dear Freesurfer experts, we have a problem with the forceps. After the first trac-all we had a forcpes minor with a really unusually structure so we tried to fix it with an rerun of the trac-all. The result was a forceps minor with a third thigh in the sagittal axis. We did a second rerun and now the forceps minor normalized. Our problem is that we don´t know if we should do more trac-all reruns by other patients with difficult tracula or how we should interpret this result. Do you have any ideas to solve this? The second problem is that we have many many tracula results with incomplete forcepes minor or major. We know that the forcepes are the most difficult tracts because of the curvature but do you have some ideas to fix that problem? Kind regards Benjamin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] DTI metrics along the whole tract?
Hi Celine - Since 5.2, there are 2 types of measures in the pathstats.byvoxel.txt file: The value at every point along the trajectory sampled at roughly the center of the bundle, or the value at every point along the trajectory averaged over the width of the bundle. Sorry, there are no other measures available at this point. If I understand correctly, you would like to see something like a profile of the measure of interest at every point along the trajectory? a.y On Mon, 6 May 2013, cel...@nmr.mgh.harvard.edu wrote: Hi Tracula team I am using tracula to study the corticospinal tract in a patient population. I am wondering if there would be a way to have the different DTI metrics from the whole tract at different depth/portion of the tracts. Something like the information given by the pathstats.byvoxel.txt file, but for the whole width of the tract? If not, do you see a way to sample the value of the diffusion metrics on a certain tract starting from the cortex (like with projfrac or projdist with the WM surface)? Thanks very much for your help Celine ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tracula error
Hi Skyler - How does the brain mask look like? Any major chunks of brain missing in the area of the left uncinate? That's the tract where the error occurs, and based on this info in the log file, I'm guessing it's a masking issue: [...] INFO: Rejected 4221 streamlines for straying off mask INFO: Rejected 2 streamlines for reversing direction INFO: Rejected 9 streamlines as length outliers INFO: Have 56 total streamlines (min/mean/max length: 1/13/33) [...] Hope this helps, a.y On Wed, 15 May 2013, Skyler Gabriel Shollenbarger wrote: Hi all, We ran tracula prep stage and it exited with errors: 'Selected streamline has fewer than 5 points'. We have attached the log and error files if needed. Thank you in advance! Skyler ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula problem
Hi Matt - Can you source try this on the command line: source dmrirc_53beta echo $b0mlist echo $b0plist Are these filenames correct, do these files exist? This is how you define them in your configuration file: set b0mlist = (`ls ${subjlist}/fmag/MR.* | sort -n | head -1`) set b0plist = (`ls ${SUBJECTS_DIR}/${subjlist}/fphas/ | sort -n | head -1`) Thanks, a.y On Wed, 15 May 2013, Hoptman, Matthew wrote: Hi all, I’m having a problem with tracula. I’m trying to run in version 5.3 beta (is that version very different from the newer 5.3?). If I run trac-preproc -c dmrirc –prep, I get: mri_convert /home/hoptman/freesurfer/subjects/c159032/ /home/hoptman/freesurfer/subjects/c159032/dmri/b0mag.nii.gz mri_convert /home/hoptman/freesurfer/subjects/c159032/ /home/hoptman/freesurfer/subjects/c159032/dmri/b0mag.nii.gz corRead(): can't open file /home/hoptman/freesurfer/subjects/c159032/COR-.info I don’t know why it would look for COR-.info in the subjects’ root directory. I’m attaching my dmrirc file in case that helps. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. __ Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.